The Whispers
by arthurignatius
Summary: The Doctor is alone. He has left Clara with a lie and is searching for Gallifrey. But he is soon drawn back to Earth by whispers of stories not staying on their pages. Fighting an enemy more intelligent than he has ever faced before, the Doctor joins forces with a second year university student who is just as lost, just as lonely and just as adventurous as the Doctor himself
1. Chapter 1

**_Because I am essentially bored with waiting for Season Nine and I have a heap of material on my laptop not really being put to any kind of use, I've decided to have an attempt at writing an entire season of fan fiction i.e. thirteen stories with an arc threading through it and a heap of original characters. I'm trying to keep, not necessarily in cannon, but certainly within Doctor Who lore. Anyway, enjoy! _**

Episode 1: The Whispers

Chapter 1 - The Boy With The Books

Someone was pounding on the door. Thomas raised his head and righted his glasses. He'd fallen asleep with them on again, sat at his desk with his head buried in _Schaum's Outline of Thermodynamics for Engineers_. He closed the book and balanced it on the ever growing pile in front of him. Before Thomas could stand, the thumping started again. As he stood and walked towards the door, he heard the sound of someone trying to activate the lock. Three shrill beeps meant there was a fault. They couldn't get in.

"Hello! Anyone in there?" The gruff greeting was followed by a murmuring and another three beeps of the lock. Thomas made an attempt at smoothing down his hair and looked back into his room to make sure there was nothing on display that was too incriminating. He opened his door to a rather bored looking man brandishing a clipboard. It was one of the porters. Thomas didn't know which one. He suspected he was new.

The porter looked Thomas up and down with a certain air of distain.

"Something's wrong with the lock on your door. The master key isn't working for some reason. Its meant to be able to unlock all the doors in the College. Oh well, I guess thats what you get when you try and bring in a new system eh?" The porter stood staring at the small black card reader on the door handle as if it were a particularly unruly student who had woken him up at three in the morning wanting him to open the College gate.

"Works perfectly fine for me" Thomas waved his own card in front of the reader on the door handle. The light flashed green and the door clicked, the lock now open. The porter frowned and ticked something on his clipboard that Thomas couldn't see before barreling past him into his room.

Thomas hung back at the doorway. He didn't like people being in his private space, let alone someone who he didn't really know. Who was now casting a rather judgemental look at Thomas' sanctuary.

"Have you got enough books? You do know there are plenty of serviceable libraries in this town. No need to amass your own" the porter scoffed before writing something else down "I might have to put this down as a fire hazard!"

Thomas looked at the porter stunned. But the porter gave another snort, indicating that he was only joking and that he expected Thomas to play along rather than take everything so seriously.

"I like them" Thomas was now glaring at the porter, daring him to continue.

The porter was right though. He did have a lot of books. The entire of one wall was hidden behind stacks of them, all neatly aligned and organised by topic, then author. Alphabetically of course. If you went into Thomas' room, you really would be at a loss to pinpoint exactly what it was he was studying. There were books on Medieval medical practices, Norse mythology, atmospheric physics, the fall of the Weimar Republic, the rise in cultural prominence of the _Carry On_ films. The goriest of horror novellas sat next to tomes of Romantic poetry. Mathematical primers were neighbours to books on neurology. Books that were banned, New York Times bestsellers and forgotten masterpieces all had a home in Thomas' room.

Whilst such a collection sounds impressive on paper, it was a little more unnerving in real life. Particularly as Thomas was perhaps one of the very few people on earth who had actually read all of the books that he owned. Thomas' intense love of learning had always separated him from his peers. There was clever, there was eager to learn, there was hardworking and there was a combination of all three. But Thomas was a little too clever, a little too eager to learn and a little too hardworking. He unnerved people. His insatiable thirst for knowledge, not just for a purpose but for knowledge's sake, drove him onwards but also drove people away from him. It was never intentional. He had tried to 'fit in'. It just never seemed to work. So to books he turned. And also to music. But mainly books.

Thomas' love of reading had not left him with the pale, slightly drawn look that typifies those who spend too long in libraries, particularly at exam times. Although very slight, he was strong and a decent runner. He enjoyed travelling and would read outdoors whenever he could. In someways, Thomas was desperate not to become a caricature of himself. His mop of unruly hair and club master glasses had earned him the nickname 'Harry Potter' to all but one person who called him 'Joe 90' instead.

Beyond the fact that Thomas owned an unusual amount of books, his neighbours and tutors didn't know much about him. No matter how curious they were, no matter how many times they googled innumerate variations of his name, no matter how many times they tried to sneak a look his contact information at the College, they couldn't find anything out. It seemed that Thomas only existed in that little room at the top of Staircase G in the right cloister of second court. Thomas liked it that way. Its not that he had many secrets that would mean anything to them, but he just couldn't bear the thought of anyone finding anything out about him that could be used against him in someway and added to the already considerable arsenal that his schoolmates had at their disposal. Thomas shuddered to think what they would say if they found out who is parents were though. He dreaded that. He knew that they were still alive somewhere. That was another good reason for remaining extremely private: he didn't want people like that mixing with the people in his College. In his eyes, they just weren't worthy of it.

In the occasional trips into is classmate's rooms Thomas saw that their pin-boards were covered in pictures of family, friends and flyers from various events and the occasional timetable or set of examples papers. Thomas' was covered in a list. Just one list, but it was long. And ever growing. He decided to write down everything that he wanted to learn and experience that year. Kind of like a bucket list. But more achievable. And without a terminal illness urging him on. That always bothered Thomas. Why do people only really start chasing their dreams when they had so little time left? Surely it would be more logical to start work on crossing things off the bucket list now whilst you still had an average life expectancy and therefore more time to get more things done. Thomas didn't just dream. He planned.

The porter noticed Thomas' list. He stared at the words for a while then turned to Thomas.

"Whats this?" he jabbed a finger at the list. Thomas moved into the room and stood level with the porter in front of the board. He was faintly embarrassed as the cluster of points that the porter was pointing to were

_258: Divine the logic behind the QI scoring system _

_259: Learn how to juggle _

_260a: Understand when exactly sexy disappeared prior to 2006 _

_260b: Understand where sexy actually went _

"Oh its a list of things I want to learn this year. My lab partner added numbers 260a and 260b. That wasn't me —" Thomas went quiet as the porter began to laugh and shake his head, but he stopped when he saw that Thomas wasn't taking it well. Maybe he was a little too quiet and sensitive. He had misjudged him and regretted giving him such an unpleasant look when he opened the door. Whilst the porter wasn't particularly fond of Thomas, or really liked him, he didn't want to upset him on his own turf. That wasn't really fair.

"Who is your lab partner?" the porter attempted to steer the conversation onto what he felt was more solid ground for Thomas.

"Ezekiel Davies" Thomas murmured. Ezekiel was clever but not quite in the same league has Thomas. Or so Thomas thought anyway. He spent too much time on the rugby pitch than at his desk which meant that there was always a frantic attempt at an example paper outside of their tutor's office. But he always did well. It was a bit galling really.

"Yeah, sounds like something he would say. Haven't seen him around for a while though" The porter did like Ezekiel. He joined in with this jokes and wasn't too much trouble. The porter frowned as he tried to remember the last time he saw him. It must have been a couple of weeks now. He made a mental note to check with his tutor as to his whereabouts, just to make sure he was OK.

"No, nor have I" Thomas replied quietly. Realising that he may have to go another supervision without him today.

"If you ever find out the answer to that QI one, let me know. I love that programme. Its so interesting you know. I love learning the stuff on that. They always make it sound interesting. I've always been like that though. Much prefer listening to things. Or watching 'em. Don't like reading though. Too much like work that. Well good luck to you"

The porter held out his hand to shake Thomas' but missed because Thomas had suddenly spotted the clock on the wall and darted towards the desk. He was late. He hastily gathered together his rucksack and pulled his laptop free of its charging lead whilst the porter looked on somewhat bewildered at this sudden burst of energy from the quiet boy. He said something about how even the cleverest people in the country couldn't keep time and laughed to himself about it but Thomas didn't hear it. He was already out the door, flying down the worn stone staircase.

"Scary to think people like him might be in power some day. Too much time looking at books. Too little time in reality" chuntered the porter as he continued his checks and went to investigate the odd hissing, almost whispering sound, coming from the pile of the only library books in the entire room "If he's burst a pipes with the weight of these books, I'll burst him"

When Thomas stepped into second court and looked up at the dull grey Thursday sky, there was nothing to indicate the fact that his life was about to be changed in a wholly unexpected and extraordinary way.

Thomas put his earbuds in and ran past the porter's lodge with Hans Zimmer pounding in his ears, through the gate and out onto the bustling street and a stream of bikes heading towards the university's main buildings.

None of them noticed the blue box lurching into reality on the corner of Trinity Street.

—

When the porter had moved the small stack of library books to the side he decided that he was starting to lose it. This must be it. The beginning of the end. The mid-life crisis, or work related breakdown, or whatever it was you were stereotypically meant to get when you were fifty.

Not only was the hissing definitely whispering, it had moved. It had moved with the pile of books. The porter picked up the pile again and moved it behind him. The whispering followed the books. He put the books outside Thomas' room and closed the door. The whispering stopped. He opened the door. He heard the whispering again. The porter picked up the pile and raised it to his ear. It was definitely the books. Although it sounded louder at the top of the pile than the bottom.

For the next quarter of an hour he arranged and rearranged the books. By a process of trial and error he found that it was Land Degradation and Society that was whispering. Which struck the porter as odd. As out of the entire pile this was definitely the dullest book. If you were going to be a whispering book, you may as well be whispering about something interesting.

The porter placed the offending book by the door and backed away. He attempted to finish his checks but the book was more than a little distracting. He took off his waistcoat and gingerly wrapped the book in it in an attempt to muffle it. Now it was comparing unravelling the causes of land degradation to murder mysteries and the porter frankly didn't want to know.

After ascertaining that Thomas was not growing or smoking anything illicit, or heaven forbid, using blu-tac on the walls, the porter decided that he had had enough of staircase G and its whispering books. He needed a lie down. Some stress related leave. And possibly a psychotherapist. But not necessarily in that order.

But before he went he decided to have one last attempt at working out exactly what was going on with that book in a desperate bid to prove to himself that he was not mad. When he picked it up, the book had become a little louder. Either that or he was more in tune to listening to it. It was now introducing the notion of "chains of explanation" to show how remote historical events are linked to specific forms of degradation. Despite himself, the porter found the subject suddenly rather interesting.

He left Thomas' room, closing the door softly behind him, suddenly thrilled at the prospect of learning about farming in eighteenth century France. Whats more was that he was actually understanding it. Him. The man who didn't have two O-levels to rub together having been plagued with dyslexia at a time when the British education system was not nearly so understanding. It was only when his Casio watch bleeped to indicate the hour, did he realise that he had been stood in the same spot, outside of Thomas' door for forty-five minutes. He looked up to see a vague outline of a person staring at him. They were stood outside, looking up at him through the latticed window. He blinked and the figure was gone. What was he thinking of? Books didn't really whisper. People didn't appear and disappear. With a sudden jerk into reality, he came to his senses.

The porter turned to unlock the door and return the book but then remembered that his card didn't work on Thomas' door. He'd just have to leave it outside. Anywhere that wasn't in his hands. But he couldn't put it down. He was torn. There was part of him willing him to loosen his grip but another part making him want to look down at the book again and read on. The book seemed to be getting closer and closer to his face. He was panicking now.

The ink on the page began to run as if it were fresh of the press and he had been caught in the rain. The porter couldn't help but stare as the ink flowed in thin streams up towards him. Suddenly his resolve to abandon the book was completely lost. The ink was moving sinuously towards his eyes. The sensation of the ink running into his eyes was like nothing he had ever experienced. As it leached to the back of his eyes, the porter's world blackened but his head was bursting with new information and understanding. He could read and comprehend better than ever before. His last thought through the agony was what a wonderful, enlightening death this was. He wished this gift had come sooner.


	2. Chapter 2

**Hello! Thanks bored411 and Uzumaki Rin for the reviews! They are very much appreciated and I hope I don't disappoint. Just a note on this chapter here, I do draw some information on the Doctor's parents from 'A History' by Lance Parkin **

The TARDIS landed with a jolt. Not her smoothest materialisation of all time, particularly as for some reason she kept wanting to land about 500 meters away from his present position. It took a lot of persuading on behalf of the Doctor for her to land on the corner of Trinity Street rather than, what, when he had examined the map the TARDIS had handily provided, looked like a student's room. As the Doctor walked towards the doors he murmured a small plea that the TARDIS had landed the right way up and the right way around as she had developed a nasty habit of landing in awkward places or positions when she felt that she needed to bring the Doctor back down to size a bit. This was now happening with alarming regularity.

Thankfully this was not one of those times. The Doctor opened the TARDIS doors to the rushing sound of bicycles whizzing past him. He suddenly felt very sad.

These people so full of life and vigour and hope and innocence were not much younger than Clara. Some of them may have been the same age. He missed her terribly, at times it was like a physical ache. In the past few years he'd never felt so alone. He'd lied to his pal and now he was paying the price. You'd think he would have learnt how to hold onto friendships by now but somehow he hadn't. He was still that lonely little boy who preferred his own company, a good book and the possibility of an adventure. After all, books didn't argue back or hold a grudge against you when you made a mistake. Although the TARDIS' library was vast both in physical size and in the range of books it held, he still thought of the small snug in his father's gardener's house as the best library in the world.

The snug could only be entered by crouching down. It had been designed for the gardener's child, who was yet to be born. He was just trialling it out for them. Once you were in the snug the room opened up slightly. The walls were covered in shelves but most of them were empty, just waiting to be filled with exciting adventures and books on mathematics, high Gallifreyian and the laws of space and time. Some books were already in place. Unlike the books in his father's house, these books were old. Their spines had been broken, the pages had been thumbed and the paper had taken on a yellow colour and a musty smell. But the Doctor loved them because they were loved. The gardener had read and re-read the books and he wanted his child to experience them too.

It was in this little snug that the Doctor first read about Earth. The gardener used to work for the High Council so had a small stack of books that he had managed to sneak out of his workplace and back home. One of these books was about Earth. The Doctor's mother was human so he knew a little of his mother's home and some of the stories. But in this snug he really learnt about the ingenuity of humanity. Their eternal hopefulness and propensity towards disaster. This little room, in a run down gardener's house, was where the universe opened up for him. Two years after he first sat in the snug, looking out of the small circular window to the swathes of red grass below, the Doctor enrolled at the Academy and his journey towards becoming a Time Lord began.

But he never forgot that snug. Or that house. Or the gardener and his wife. They were always the people who came and comforted him. The first time he had 'the nightmare', they were the ones who made the long walk from their house to the small isolated barn to check if he was OK. They somehow understood him in his isolation, far more than his own parent's ever did. They understood that he felt different and they empathised with that. It was one of the Doctor's greatest regrets that he always failed to see them anytime that he returned on Gallifrey. Even now, he still daydreamed about telling the gardener that he had made it., that he had explored the universe and saved worlds. But more than anything he wanted to say thank you. Because after all, some of the best teachers that we come across in our lives aren't always found in classrooms.

The Doctor was touching his ring, feeling a little lost. He needed to find someone again. Someone who wouldn't mind him making mistakes and who would want to stick around. This time, he decided, he was going to make the effort. He would really try to understand this person and try and make them understand him. But first there was a task at hand.

The Doctor set of walking at quite a pace, heading up Trinity Street. He needed to give a book back and it was hideously overdue. Sometime during is third regeneration he had taken out a book on Jeremy Bentham's panopticon for some reason that has now been lost in time. Normally the Doctor took no notice of return dates but this particular book had started behaving, well, a little oddly. Which was certainly saying something. After all it was wedged on his shelf between a book whose ending changed depended on your mood and Philip Larkin VIII's galactically best selling trilogy of "Parenting's Greatest Mistakes", "Some More of Parenting's Greatest Mistakes" and "Why Do We Bother With Children Anyway". The book that was now in the Doctor's pocket had started whispering. There were plenty of whispering books in the universe, but this one wasn't one of them. No book from Earth was meant to whisper. Not any more anyway.

On the other side of the road, Thomas was hurrying towards his supervision. On the one hand, he really didn't want to be late, but on the other he really did not want to go. He was hoping beyond hope that Ezekiel would suddenly appear from wherever it was he was lurking and come and join him. Being along in a supervision would mean that he would have to speak. And being alone with Professor Oakley would mean that he wouldn't be let off the hook. Oakley, like most of the other people in his College, viewed Thomas with suspicion. But Oakley went one step further. He kept an unnervingly close eye on Thomas and recently this intense scrutinisation had ramped up. Over the past month, just before Ezekiel decided to disappear, Oakley had been finding odd reasons to visit Thomas in his College. He was always bumping into him in the streets and even, on more than one occasion, Thomas had found himself sitting across from Oakley in the University Library.

Thomas crossed the road and followed a tall, wiry man in his fifties through the gate of Trinity College. The man lifted a pass up to the porters on duty and was allowed through. The porters were so used to seeing Thomas by now that they didn't ask him for identification, instead waving him through.

First Court of Trinity College was impressive. Even on an overcast Thursday it never failed to be a beautiful sight to be hold. A vast rectangle of verdant green grass was bordered by yellow stone buildings. Beyond First Court was the Wren Library. In the summer, the sunlight bounced off the windows making the building seem alive. This was where the older man was heading. Thomas saw him walk ahead, in a springy, almost awkward motion before veering to the left, a flash of red lining of his coat suddenly visible. Thomas nearly missed the entrance to the staircase of Oakley's rooms as he was so fixated on the man ahead of him. He felt that he was someone important, but he couldn't quite place his finger on who.

Thomas reluctantly tore his eyes away and trudged up the stairs towards his supervision. A quick check of his watch showed that he was two minutes late, but he guessed that didn't matter. After all, its not like Ezekiel was ever that punctual. Thomas rapped his knuckles on the wooden door and a soft voice called for him to enter.

"Mr O'Mara, two minutes late I see. Well, I you can't be perfect at everything I suppose" Oakley offered Thomas a small smile. Thomas didn't return it

"Sorry" Thomas murmured, not quite meeting Oakley's eyes. Oakley merely chuckled quietly. Oakley did everything quietly. He was the sort of person who never seemed to get angry but everyone lived in fear of the moment when he would finally snap as it would probably be catastrophic. He was too calm and too kind to be true. Even if he was wary of Thomas. Oakley motioned for Thomas to sit down and started cleaning his glasses, looking at Thomas as if a parent was surveying a troubled child.

"I'm only teasing Thomas. You would do well not to take the world so seriously. After all, when you think about it, it really is quite a silly place. Now, onto your essay. Very good as always. But there is a fair amount of constructive criticism I can give. We have an hour, well fifty-eight minutes now, and the worst murder a man can commit is the killing of time. So lets not waste what we have and crack on shall we?"

Whilst Thomas was being grilled over the finer points of his work, the Doctor wasn't having much joy either. Upon entering the library and enquiring at the small desk, he discovered that the librarian with whom he had originally checked the book out had died twenty years ago, crushed under a pile of books when a shelf with wood-rot collapsed on him. The Doctor had to remind himself that humans neither had the life span or the rejuvinative capacity of Gallifreyans. The second annoying discovery of the day was the book he was holding, whose whispers had now risen to murmuring, no longer lived in the Wren Library. A new run of the books had replaced the old version. The older versions were now consigned to the bowels of the University Library.

Not one to waste a journey, the Doctor decided to hang around and see if any of the books in here tended towards whispering. Hidden between two rows of economics books, the Doctor took out is sonic screwdriver and began to scan for whispering books. As he wandered around the library, he found nothing, except for Bentham's book now safely stowed away in his pocket once more. After he had done a thorough sweep of the building he decided that now was the time to probably call it quits and move on. But before he did he corrected a couple of errors in an essay that a wandering student left behind on a desk.

The Doctor was walking back towards the main gate when the sonic screwdriver started buzzing rather loudly. It took him a minute to work out whether this noise was the automatic reminder that he'd left the kettle on or if there was an a-typical sonic frequency emitting from a paper and ink formation. He decided it was the latter. The Doctor walked towards a small entrance way in one of the buildings surrounding the court and the buzzing intensified. There was another whispering book somewhere on this staircase. As he ascended the stairs the Doctor vaguely thought that he should probably be a bit nervous about what he might find. But he decided against this as a lack of caution hadn't done him any harm in the past. Well, it hadn't done him much harm lately.

The Doctor was now standing outside a door with the name "Prof. G.O. Oakley" emblazoned above the door. There were two people talking inside. The Doctor turned off the sonic screwdriver and barrelled into the room. He stood the doorway for a moment, the surprised faces of Thomas and Oakley staring up at him. Oakley opened his mouth as if to say something and then closed it again. Thomas just kept staring. It was that man, the one who he'd seen go into the library. Although he was old, he had an air of youth and energy about him. His eyes were bright and alert, scanning the room for something. His slim figure, dressed in black, looked primed and ready to run at any given moment. It was an odd contrast to Oakley. Oakley was much younger but somehow always looked older than he was. His eyes were blue too and although bright held a definite air of sadness and loss. He was slow moving, slow talking. Nothing was a rush for him. But this man in the door, who still had not said a word, was advancing towards a pile of books to the left of Oakley's desk.

It was only when the Doctor started rummaging through the books and holding them up to his ears that Thomas felt compelled to ask him

"What are you doing?" Thomas enquired

"Shh! Listening!" the Doctor replied, almost irritated. But he reprimanded himself. After all, it was less than an hour ago that he had made a silent pledge to himself to make more of an effort to be nice and understand people.

"To the books?" Thomas continued. He had now got up and was moving to join the Doctor, who was now crouched low on the floor

"To the books" The Doctor grinned and Thomas, almost despite himself, grinned back.

Oakley was less surprised at what the Doctor was now doing than the fact that Thomas had taken the initiative to speak to this stranger. Oakley, and indeed anyone else who taught Thomas, had a tough enough time getting him to talk to them let alone someone entirely new and unfamiliar! By now the Doctor had scooped up the pile of books and was balancing them awkwardly in his gangly arms.

"Could you please?" the Doctor nodded to the door and Thomas moved to open it for him. As the Doctor disappeared down the stairs, Thomas and Oakley moved to the windows to watch his progress across First Court. Once they saw the Doctor had exited through the gate, Thomas turned to Oakley who merely shrugged as if strange men were continuously entering his room to steal away overdue library books.

"Professor?" Thomas said timidly, Oakley walked back to his desk "Who was that? Why did he do that?"

"Oh I don't know. But he probably knows what he's doing" Oakley waved his hand dismissively as he spoke, the apparent initial shock had now more than worn off "Now, how about working out a title for next week's essay?"

Oakley's phone buzzed on his desk. He picked it up and read the opening two lines of the text on the lock screen and his face paled. Thomas was still stood with his back to Oakley, looking longingly out of the window and wanting to follow the man with the wicked grin and those bright blue eyes.


	3. Chapter 3

**Hi all! Sorry for the hideous gap between updates but I've been busy with exams, exams, oh and whats the other thing? Exams. As soon as June finishes I am free. Woo! I've also managed to scope out how this series will end so everything now will hopefully have a nice logical flow to it with a few twists along the way. Many thanks again to those who favourited/followed and a special thanks to the reviewers bored411, I Am The Eleventh and nebu1a. You guys brighten up my otherwise drab inbox. Have lovely evenings and great weekends, A x **

**Chapter 3 – Educated Guessing**

Oakley unlocked his phone and read the text, letting out a breath he didn't realise he was holding. Thomas was still stood at the window, gazing out over First Court. That boy was eerily still. In light of what Oakley had just read, the stillness was almost menacing. Oakley stood up slowly, approaching Thomas as if he might be easily scared off. Oakley wasn't scared of Thomas. He had faced worse men than him. But he was scared of Thomas might do to himself and what he had done, and might yet still do, to others. The clouds over First Court seemed heavier now, Oakley observed, it was as if the sky itself knew the significance of events below.

Oakley and Thomas stood side-by-side looking out over the green court. Thomas' eyes held a far off look but Oakley's were steely, boring into the side of Thomas' head, still angled towards the window. Oakley reached out to touch Thomas' shoulder and gain his attention but the moment that his fingers brushed the student's shoulders, Thomas jerked away as if burned. The unfocussed eyes now looked alarmed and his body was tensed in an obvious fight or flight mode.

Oakley raised his hands and Thomas relaxed, although the wary looked remained.

"I only wanted your attention" Oakley said "Nothing more. Are you OK Thomas?"

Thomas gave a slight nod and made a move to retake his place in front of Oakley's desk.

"Don't worry about the essay Thomas" Oakley said. Thomas looked confused "If there is anything you need to tell me, you know that you can. I can't promise confidentiality but we all make errors in judgement and I'm offering you some support. But this is a one time offer"

Thomas' slight confusion had now entered the realm of total bewilderment. What on earth was Oakley talking about? Oakley had always been so suspicious and somewhat distant and now he was offering Thomas support? But support for what? Oakley's sad blue eyes had locked onto Thomas'. Thomas tried to avert his gaze but he couldn't help himself.

"Professor, I…" Thomas began, not knowing quite how to continue. Oakley looked almost pleadingly at him but the familiar suspicion was beginning to return. Thomas felt like he was being cornered. For the second time that day Thomas hastily picked up his bag from the floor and made a swift exit, taking the stairs down to First Court two at a time.

Oakley picked up his phone from the desk and re-read the text before dialling the sender, returning to his watch over First Court. The phone only rang twice before it was picked up.

"Do you have him Oakley?" the voice was as clipped as usual, emitting a cool, harsh calm and control. Oakley closed his eyes and raised his hand to his brow. Today was going to be a long day.

"He's just left" Oakley's voice was as soft as ever, remarkable really considering the circumstances "He's definitely involved of that I'm sure. Promise me you'll get him this time before he does anything else. For all our sakes" Oakley ended the call and pocketed the phone, running his hand across his greying beard as he watched Thomas' progress across the court. The boy was running and only two types of people ran. The scared and the guilty. Oakley was pretty sure that Thomas was both.

Thomas was pelting across First Court desperate to put as much distance as he could between himself and Oakley. He didn't really understand exactly what had just happened but he knew that he shouldn't dwell in that room for any longer. He needed to find the man with the books. When he made it out onto Trinity Street and back into the flow of students, townies and tourists a wave of despair came over him. The man was nowhere to be seen. Cursing slightly under his breath he headed back towards his college, once more passing the blue box on the corner of Trinity Street without a second glance.

"Think" Thomas muttered to himself "Come on. Think your way out of this. Its what you do best. Work it out. Take it a step at a time"

Thomas drummed his fingers on his leg as he worked through exactly what he knew. He discarded anything that wasn't concrete fact. Never twist facts to suit your theory. Twist theory to suit your facts. By the time that Thomas had reached the bridge he had almost formed a theory in his head. He picked up his pace a little and instead of taking a right turn towards his rooms, he took a left and headed to where his bike was parked.

Thomas loved his bike. It was a sleek black and although it was second hand, bought only for £90 from a shop near the station, it looked and rode like new. As he rounded the corner to the bike store, he saw the tall, twisted figure of his neighbour unlocking their own bike. Harley Lauda. And much to Thomas' dismay, he saw that Harley's bike was next to his own. Harley was probably the closest thing that Thomas had to a friend but there were certain times, and now was one of them, that Thomas really didn't feel like talking.

"Apparently there's a load of people looking for you O'Mara" Harley said, not looking up. Thomas was taken aback slightly. He had thought he'd come in unnoticed, apparently not "Porters, police, the lot. If I arrested you, I'd probably get a medal pinned on me. But I won't. Partly because I'm nice like that. But mostly because I'm late. I'm a worse timekeeper than you"

Harley finally looked up to find Thomas looking even more confused than before. The police? Why were the police looking for him? Harley had now unlocked the white Peugeot bike and was going about stowing the keys back in the black Osprey backpack on their back. Once done, Harley stood up straight and looked Thomas squarely in the eye. They couldn't have been silent for more than ten seconds but it felt like hours. The bike store was eerily quiet. Usually at this time of day there were students coming and going the entire time but for some reason no-one was avoiding the peace of the inhabitants of Staircase G.

"What do you mean the police?" Thomas asked, tearing his eyes away from Harley and now entering the combination into his own lock.

"Surely you'd know more about that than me" Harley said nonchalantly "They're looking for me as well, so don't go thinking you're special"

"What did you do?" Thomas straightened up again and wound his lock around the frame of his bike

"Nothing" Harley shrugged " What did you do?"

"Nothing" Thomas' voice was even quieter than usual

"Well, one of us is lying" Harley smiled and pushed off, one leg swinging over the bike as it pulled away. Thomas was left standing in amongst the hundreds of bikes in the store. He looked up to the greying sky above him, a stark contrast to the bright white walls that surrounded him. Whatever was going on wasn't good and he certainly needed to distance himself from whatever it was. Pronto. People in college treated him with enough suspicion as it was, never mind getting the police involved. Thomas walked his bike back to the main road. Across from him he could see a small huddle of porters and fellows outside the porter's lodge. There was a police officer with them and a woman who Thomas suspected was some kind of DI or Sergeant. She was in plain clothes that verged on a masculine style with cropped blonde hair. None of the group noticed Thomas. But Thomas had certainly noticed them.

Thomas hastily mounted his bike and headed towards his destination. Time to put his theory to the test. He prayed to whatever god that was listening that he was right.

Less than half a mile away the Doctor was walking slowly down an aisle of books, the sonic screwdriver in one hand and his overdue library book in the other. He'd left the small stack of books that he had picked up in Trinity at the beginning of the shelves he was now walking in-between. The screwdriver was alerting him again to the presence of whispering books. This time he was certain he hadn't left the kettle on. The whispering was growing in strength the further down the aisle he walked.

It hadn't taken the Doctor long to work out that this was the specific area in the University Library that he was looking for. These books weren't old but they weren't new either. Most copies were published in the late twentieth century and had previously belonged to other libraries before they found their home in an obscure little aisle in on of the country's only copyright libraries.

As the Doctor progressed even further into the library, he noticed that it was becoming darker and darker. He stopped abruptly and did a quick scan for Vashta Narada but it came up negative. He didn't think it was the forest dwellers but in this particular instance he would rather be safe than sorry. He smiled to himself and almost turned to Clara to tell her about The Library and River Song and Proper Dave and Other Dave and Donna and C.A.L. but he couldn't. Because she wasn't with him anymore. A pang of sadness came over him for the second time that day. He needed to find someone.

As if on cue he heard someone knocking on the metal shelves behind him, as if someone was knocking on a door.

"Excuse me" said a small, but somehow determined voice behind him "Can I help you?"

The Doctor turned round and walked back towards the lighter end of the aisle where a tall, slim bespectacled boy with a mop of unruly black hair was standing. He was shifting his weight awkwardly from foot to foot. The Doctor thought he recognised him from somewhere.

"I'm OK thank you. Just browsing" The Doctor replied and made to walk past the boy but he stopped himself when the boy spoke again.

"You were in Professor Oakley's office. You were seeing if the books were whispering. I came to find you" Thomas' voice was more assured. The office at Trinity. That was where the Doctor had seen him before. But even when he had made that connection, he somehow felt that there was something more. Where else had he seen him?

"Why did you come and find me?" the Doctor asked, trying not to sound too defensive.

"I just –" Thomas started, the initial confidence now abating somewhat "I wanted to find you"

"You wanted to find me?" The Doctor replied

"Well I want to know why the books were whispering and if you didn't know why they were whispering I was going to help you find out why" Thomas felt himself blush and he was suddenly very embarrassed, particularly as the Doctor was giving him a rather strange look.

"How did you know I would be here?" the Doctor asked, pocketing his sonic screwdriver

"I didn't. It was an educated guess" Thomas said and the Doctor motioned for him to continue "Well, the books that you were listening to in Professor Oakley's room were library books. They had the University Library sticker on the front. You weren't interested in any of the others. If you wanted to find more books that whispered, you'd come here"

"You're good. You know that?" the Doctor said and Thomas blushed slightly, shrugging is shoulders in an effort to look cool rather than immensely proud of himself and pleased that he had impressed this stranger which is what he was really feeling. Thomas got the sense that the Doctor could tell that this was the case, but instead of calling him out on it, the Doctor managed to portray a sense of understanding. "Books shouldn't whisper. But for some reason, this little batch of books is. I know what is causing the books to whisper but I don't know why. I don't know why now and I don't know why here"

The Doctor motioned for Thomas to stand next to him.

"You see that?" The Doctor asked, motioning to the darkened end of the aisle

"I don't see anything, just that it gets darker" Thomas said, worrying slightly that he had got the answer wrong

"You're right. It gets darker. But why?" the Doctor asked Thomas, the wild blue eyes that had captivated Thomas in Oakley's office making a return

"Possibly some kind of electric fault, lights not working maybe?" the Doctor looked at Thomas as if to say 'you can do better than that'. Thomas felt like he was undergoing the hardest, yet most interesting supervision of his life "But it can't be the lights because they are working. I can see the light on the ceiling working but there is darkness below it that the light isn't penetrating. Therefore, whatever is making it dark must be something else. The only other things down there are books. Therefore…its the books. The books are making it dark"

When Thomas had finished the Doctor took a step back and looked the boy up and down. That was where he recognised Thomas from. Thomas was just like him. A little shy. A little awkward. And more than a little clever. The Doctor hadn't just seen Thomas in Oakley's office, he'd seen himself in him. The Doctor thought, somewhat whimsically, that had Thomas been on Gallifrey when the Doctor was growing up, maybe the two could have been friends.

Thomas mistook this silence for some kind of judgement and an indication that his theory was as ridiculous as it sounded.

"Ignore that. That's impossible. Books don't create darkness" Thomas was shaking his head and the Doctor began to chuckle.

"Nothing is impossible" he held his hand out to Thomas "I'm the Doctor"

Thomas smiled and took the older man's hand

"I'm Thomas"


	4. Chapter 4

**Thanks for all the new ****favourites and follows - very much appreciated. Special thanks to those who reviewed (bored411 who makes the hattrick reviewing all three chapters so far and nebu1a). Mildly shorter chapter this time but I've been a bit pushed in terms of workload. It would be really great to get a beta reader on this - any recommendations or offering of help would be much appreciated! Anyway, now that the slightly admin-y bit is done, onwards with the Doctor and Thomas! Hope you're all having great days, A **

The Doctor let loose his hold on Thomas' hand and spun back around to face the aisle of books. A whisper was coming from the far end of the row. The Doctor edged forward, his boots creaking slightly as he moved. He reached into his left coat pocket and rooted around for the sonic screwdriver. He felt the cool metal casing and pulled it out, aiming it at the whispering darkness in-front of him. Thomas watched confused as the Doctor began scanning the space. The green light at the end of the device was having no impact on brightening the row of books. The dull hum of the screwdriver wasn't giving anything away either.

"Why-" Thomas started "I mean what…are you? I mean is that…?"

"Sonic screwdriver. Very good at assembling cabinets. But also scanning for alien tech" the Doctor replied, finishing his sweep of the area. He looked at the screwdriver with a puzzled expression, shaking it twice and holding it up to his ear before stowing it back into his coat and slowly backing away from the whispering books

"Alien?" Thomas asked, following the Doctor who was now walking at a very brisk pace back towards the lifts at the centre of the library floor. As they walked across the space Thomas noticed that it was unusually quiet. Where was everyone?

"Yes. You know…not of earth. You've had enough of them around over the past few years for you no longer to look surprised at the mention of the world alien. Which is what's odd about this whole situation. Other than the fact that we have an entire row of Geography books chattering away and a darkness that isn't penetrated by light"

Thomas now had an expression on his face that the Doctor was having trouble interpreting. There was a definite flash of panic there mixed with something else.

"W-whats odd about me?" Thomas stuttered, falling just slightly behind the Doctor.

"Not you. These" The Doctor gestured at the stacks and stacks of books surrounding them before jabbing his finger to call the lift. Thomas looked somewhat relieved and let out a breath that he didn't realise he was holding. Thomas knew that the Doctor would find out the truth about him one day but he wasn't ready for that just yet. He wanted the Doctor to get to know him first. Thomas had now caught up with the Doctor and entered the lift. The Doctor was leaning casually on one of the walls of the lift, arms crossed and emanating an effortless cool that Thomas had only ever seen in one other person; Harley. Thomas' mind drifted back to his encounter with Harley in the bike park. In his thrill of finding the Doctor he had almost forgotten the small huddle of people waiting to find him at the Porter's lodge. Thomas debating whether or not to tell the Doctor but he decided against it. Instead he opted for another question.

"You mentioned alien. And then said that that wasn't odd. So what was odd?" The lift arrived at the ground floor and the Doctor and Thomas swept out

"Well, the thing is, Thomas, is that you would expect whispering books to be alien. You would expect them not to be on Earth. But when the sonic screwdriver scanned for alien tech, the reading was negative. These books, they are meant to be here. They are of earth" The Doctor was now walking at a very brisk pace, turning left and onto the small path back towards the centre of town.

"But I've never heard of whispering books on Earth before" Thomas said. He and the Doctor came to a standstill whilst Thomas unlocked his bike from the railings lining the path. A small group of chattering students flew past the pair, unaware of the strange goings on happening mere meters away from them. Thomas wondered how many of them would be going towards the library and the Geography section. More specifically the section on Political Ecology. Surely that won't be that many people? They shouldn't be in too much danger? Should they? The small lane was quiet once more.

"Whatever this is, its obviously a contained phenomenon. Its only affecting books in that section of the library" The Doctor replied, eyeing Thomas' bike with a look of repulsion. To him it looked like an incredibly dangerous and inefficient method of transport.

"Two things" Thomas said, once again, stowing away his bike lock "One. Shouldn't we tell someone?"

"No" the Doctor replied "You don't expect me to ride that do you?"

" . They're in my room" Thomas said

"What?" Now it was the Doctor's turn to look confused

"Books. From the University Library. That section even. I have them!" Thomas was now leading the way, leaving the Doctor to catch up.

"You study Geography?" Thomas didn't know whether or not to take the Doctor's slight tone of surprise as a positive or negative

"No I -" but Thomas never got to finish his sentence. A thin black liquid was running off the bottom of the Doctor's coat creating a small pool on the grey tarmac path. The Doctor looked down to see what Thomas was staring at. He cautiously dipped the toe of his boot into the small black puddle forming at his feet. Ink.

The Doctor quickly took off his coat. As it fell to the floor Thomas could see that even some of the vivid red lining had been stained black. Thomas shoved his bike into the Doctor's hands and crouched down, slowly turning the coat over. The ink was definitely coming from one of the pockets. He was about to reach in when the Doctor whispered at him to be careful. His voice was hoarse and Thomas looked up to see the older man look something between concerned and impressed at him. This only served to encourage Thomas

"I'm fine" He said, his voice more assured than he felt "I've got this"

Thomas turned his attention back towards the coat, the pool of ink steadily growing in size. He put his hand into the pocket and felt around. To his surprise, at first he couldn't feel anything. He thrust his hand further in and after a few seconds waving it around, he came in contact with a cool, cold liquid. Thomas moved his hand further in. How big was this pocket? He was about to pull his hand out when he found it. A solid object that was soaked through. He gripped it as best he could and yanked it out of the coat an onto the pavement. It was a book. Just faintly discernible through the black ink was a university library sticker. Thomas managed to separate two pages but instead of text on the page. It was blank.

"It's not the books themselves that are dangerous. The paper and bindings are fine. Its what's written on the pages that's dangerous" The Doctor said, staring down at the book as Thomas slowly stood up "Words are dangerous dangerous things. The right words in the right combination can save worlds, make people fall in love, bring hope and clarity to desperate and confusing situations. They can reach out across time and space and take a hold of you, connecting you to another person in a way that is entirely unique and entirely compelling and moving. And yet they can also make you feel hollow, compel you to commit heinous acts and destroy you within mere moments"

"What about these words?" Thomas asked "What will they do?"

"I don't know" the Doctor said "Not often I say that, but this time, I really don't know"

Thomas took a step back. The ink appeared to follow him. He took another and the ink moved again. The ink was now no longer just running along the floor in a random pattern, it was definitely snaking towards Thomas.

"Its latched onto you" the Doctor said, crouching down and trying to find the sonic screwdriver without touching the ink. Thomas was now backing away a little faster whilst the ink seemed to be beginning to form some kind of three dimensional shape. He looked wildly around to see if anyone else was watching. Should he warn them to get away? But no one was there. Thomas thought that he could see one bike approaching in the distance but whoever it was took a right, away from himself and the Doctor.

"Run" the Doctor shouted, taking Thomas by surprise. It took a fraction of a second longer than it should be when Thomas saw the wave of ink heading towards him, he didn't delay. He sprinted away from the Doctor down towards the centre of town. He could hear the Doctor shouting him onwards above the sound of the black liquid swishing after him. It appeared that the ink was matching his own speed. If he sped up, so did the ink. Thomas didn't want to know what would happen if he slowed down.

Thomas chanced a glance back and saw a wall of black ink, his own height directly behind him. But what was more frightening was not that the ink had somehow learnt to defy gravity but it had taken on the rough outline of a human. It even had two sunken sockets where eyes would usually sit. Thomas picked up his pace again, wondering where on earth the Doctor was. Why wasn't he helping?

The end of the path was fast approaching; he was about to come to the main road. There were going be people. He had to guide the ink away somehow. Thomas glanced around him. There was a brick wall to his left but railings to his right. Beyond the railings was woodland. Maybe he could climb the railings and move the ink to somewhere more isolated, giving the Doctor time to catch up. Thomas had no reason to believe that the Doctor could, or would, come to his aid and save him but deep down, Thomas just knew that the Doctor would appear. He would help and he wouldn't abandon him.

Thomas veered to the right and reached out his arm to grasp the railings. The Doctor was still stood in the middle of the path next to Thomas' bike now resting against the railings. The ink had now entirely left his coat leaving it unstained. Just like new. He picked it up and put it back on. It was much easier to find the sonic screwdriver this way. The Doctor saw that Thomas had changed courses slightly.

"No!" he shouted "Keep running straight Thomas!"

Thomas must have heard him as the young man corrected his path and once more was heading towards the main road. But what was more important was that he was heading towards the storm drain. The Doctor picked up his bike and walked towards Thomas.

At the other end of the path Thomas' heart was pounding. He trusted the Doctor but why did he want to lead it towards the main road? Thomas found himself at the crossing. He raced across, hardly noticing that he was almost hit by two cars and a bike. Once he reached the other side he kept his pace up. But he was only moving for a couple of seconds before he realised that the rushing sound had skidded to a halt and turned on his heals. The Doctor was stood on the other side of the road, looking quite calm, the sonic screwdriver on one hand with Thomas' bike balanced on his hip. He free hand was motioning to the floor. Thomas looked down.

The storm drain.

Thomas smiled and crossed back to meet the Doctor. The Doctor handed Thomas his bike back as well as the now blank book that the Doctor drew from his pocket.

"Don't worry about the ink in the drain. It will be diluted down. That stuff is only dangerous in its purest form. Well technically it isn't dangerous at all" the Doctor said. Thomas was just about to ask him to stop talking in riddles and actually tell him what was going on when he was stopped by the Doctor clapping his hands and motioning Thomas away "Well you said they were in your room, so there is a blank copy of what you are looking for. Go and find them and when you've got them bring them to me. I'm going back to Oakley's room. I need to check that I picked all of them up. Can you do that?"

Thomas nodded, placing the blank book in his backpack and mounting his bike.

"Where shall I meet you?" he asked

"The corner of Trinity Street. There is a bright blue police box. Come and knock on the door and I'll let you in" the Doctor replied and Thomas nodded.

"Just one more thing Doctor" Thomas said "Those books, they were Geography books. Oakley is not a professor of Geography. So why then did he have the books in his office?"

"I don't know" the Doctor shrugged "Why do you have them?"

Thomas opened his mouth to offer a response but closed it again. The Doctor shrugged once more and crossed the road to walk back towards Oakley's office. Thomas stood and watched the older man leave. Despite the danger that Thomas knew that he was in, he couldn't help but feel a little thrilled and a little elated. For the first time in years he felt like he was really living. He was definitely still guarding himself a lot though. He wanted the Doctor to like him after all.

As Thomas mounted his bike there was a flash of lightning. Thomas counted to twelve. A clap of thunder followed. He looked up to the darkening sky and preyed for the storm to hold off, just for a little longer. He had a job to do.


	5. Chapter 5

**Hello all! Exam season is over! Incredibly pleased about this as I can start enjoying the summer and getting to churning out plenty of writing. Thanks once again for favouriting and following. Shout out to the reviewers Uzumaki Rin, bored411 and The Wizard's Daughter . I'm really glad that you like Thomas :) x **

As Harley Lauda cycled away from her lecture, an uneasy feeling was settling itself in her gut. As she came to a standstill on the road outside the department, Harley could feel people staring. Reaching around into the back pocket of her rucksack she pulled out a pair of black rimmed sunglasses and put them on. The traffic began to move once more and Harley pushed off, keeping a safe distance between the bright red bus in front of her and her own bike.

Harley simultaneously loved and loathed cycling through town. When going full speed with the wind in her hair it felt like flying but on days like today when the roads were crowded and it was threatening to rain with the wind picking up, Harley would much rather walk. But she didn't have the time today. She had too much work to do. As if to remind her why she was running behind a shooting pain ran up her left arm and up her neck. Harley gritted her teeth and managed to keep her bike straight. It had bothered her all last night and whilst she could work, she hadn't got nearly as much done as she would like. And now she was behind schedule.

The traffic came to a halt again. A dozen bikes came to rest next to Harley. Harley gingerly touched her left arm. It was years since her accident. Everything else was now painless except this. The girl on the bike next to Harley was casting her a worried look.

Whilst, like Thomas, Harley was tall but unlike Thomas, no one could really look at Harley and say that Harley was good looking. The entire of the left half of Harley's body had evidently been through a trauma that many at college struggled to imagine. Harley's left arm was twisted in too close to her torso to possibly be comfortable. Harley's hands were also odd with all but two fingers on each curled into her palms and locked their. But what was most striking about Harley was her face. Cutting across Harley's left eye was a dull red scar in a perfectly straight line. The eye that it cut across was obviously blind. The pupil was far too large and in the inky black were flecks of white. Harley's other eye was a dull hazel colour with dashes of orange that were only visible in the sun. Thomas slightly wished that Harley wouldn't always wear sunglasses so that the rest of the world could see that as it was really rather beautiful. He may or may not have told Harley that on one of the very few occasions when he had had one too many to drink.

But what Harley had that Thomas definitely lacked was friends. A certain effortless cool with a charm and ease seemed to follow Harley about wherever they went. At first, somewhat pessimistically and some would even say cruelly, Thomas thought that this popularity was underpinned and ultimately driven by pity. But as time wore on he saw that the majority of the college's population had gotten over their initial shock and, in certain cases, revulsion and seen past the scars and the twisted body and found someone who was genuinely warm, genuinely kind, genuinely funny and genuinely brave.

"Are you OK?" the girl asked over the roar of the traffic in the opposite lane

"Yeah, I'm alright" Harley replied, giving the girl, a small smile

"Hell of a party was it? You take a drunken fall?" the girl asked, pointing to Harley's arm and face

"Something like that" Harley said, unsmiling this time. The traffic began to move again and the girl sped off. Harley followed her but when she reached the corner of Trinity Street she heard a distinct whispering, coming from somewhere that Harley couldn't locate. It sounded like the sound was all around her. Harley dismounted her bike and rested it against the wall. The sound followed her and was growing in strength. Harley took her backpack off and began rummaging through it to try and find the source of the whispering. Surely it was going to be in the bag. This couldn't be in her head, could it? Could it be that after everything she had finally snapped? That was the question those men and women were asking her earlier that day.

She had reached the bottom of her bag, all that was left in it was her laptop, sketchbook and a solitary book. It couldn't be one of them could it? She checked that the laptop was completely turned off and it wasn't making any noise. As she picked up the book and flicked through it, a bolt of lightning cut through the sky and Harley snapped her head up, looking straight ahead as the space in-front of her was illuminated. The whispering stopped.

Across town the Doctor glanced back to see Thomas mounting his bike and riding back towards his college. There was something about that boy that the Doctor couldn't put his finger on. Maybe it was that he felt like he was so much like him? He even looked a little like some of his earlier selves with the mop of unruly hair and dull grey eyes. Although his weren't hidden behind a pair of glasses. Could this boy really be the next Clara? The air around the Doctor began to feel heavy. He looked up at the charcoal sky. A storm was certainly on its way.

The Doctor had not intended to spend long in Cambridge at all. He fully expected to drop off his book, find the source of the whispering and leave all within the space of half an hour. But time was ticking on now. It was coming to the end of the afternoon.

The wind was beginning to pick up again, rustling through the trees lining the path that the Doctor was taking back into town. The Doctor turned his coat collar up and stuffed his hands into his pockets and leaning forwards slightly against the now driving wind. He briefly thought about how Thomas was managing to keep his balance on the flimsy looking bike in this kind of weather. In a moment of almost paternal panic he suddenly remembered that he had not seen Thomas put a helmet on. The Doctor then mentally told himself to get a grip. The boy wasn't his son after all. The Doctor's right hand drifted back to touch the ring on his left.

Lost in his thoughts the Doctor suddenly realised that he was at a crossroads. After a moment's hesitation he turned left and down a smaller passage. He was sure that this was the quickest, if not slightly illicit, route into Oakley's college. The Doctor ducked under a wooden gate and into the gardens behind the Wren Library. Across the lawn he could see a small huddle of students quickly gathering up their work and heading inside. Another bolt of lighting cracked through the now almost black cloud cover followed by another low rumble of thunder. It was definitely going to rain.

The Doctor made his way back towards Professor Oakley's rooms. Even in this dreary weather and more than troubling circumstances, Cambridge was utterly beautiful. All over the world and throughout time other universities tried to imitate the architecture and the atmosphere of intense learning but none had quite got it down to a tee. There were always slight errors.

Turning into the staircase to Oakley's rooms the Doctor nearly fell over a cleaner dusting down the stairs.

"Oh I am sorry" the cleaner said. She was a middle aged woman with the college's cleaners uniform on "Not seen you round here before"

"Err no" the Doctor said, still recovering from the initial shock of nearly trampling a woman "Can I just -" the Doctor moved to walk past the cleaner but stopped when she gave an exasperated huff.

"I've just cleaned that!" the cleaner motioned at the stairs "and anyway it will be a wasted journey. No-ones upstairs"

"How do you know Oakley isn't up there?" the Doctor asked, trying his upmost to keep his patience

"Sorry, Oakley?" the cleaner looked momentarily confused whilst she removed her Marigold gloves. The Doctor had the uneasy sensation that this was not going to be a short conversation

"I'm afraid its rather urgent" the Doctor said almost a little too tersely but the cleaner clearly hadn't picked up on this and continued on.

"Oh yes. Sorry! Senior moment! Not used to hearing him called by his second name. Usually only his first you see. He's not in I'm afraid. Just popped out. Looked a bit preoccupied mind. But maybe that's because he was worrying about treading on a bit I'd cleaned. He's very nice like that. Very considerate man. Although somehow sad. I've always said that. In fact I was only saying to our Marie the other week, "Marie, what that man needs is the love of a good woman". That would see him right I'm sure. He looks like he's had is heart broken one too many times that one. There was another professor just like that but then it turned out that he -"

But before the cleaner could continue her dissection of the love life of the senior academic staff of the college the Doctor had finally snapped and marched up the stairs. He could only feign interest for so long after all. As he ascended he heard the cleaner shout up to him but his mind had already filtered her voice out into his mental 'spam' box.

The door to Oakley's room was firmly shut. The Doctor gave the wood an experimental push and found that it was open. He pushed slowly, poking his head around the door. When he saw the coast was clear he opened the door wide and stepped into the room. He was a little more wary of Oakley than he had been earlier that day.

Oakley's room was rather small and the Doctor saw that there was a door at the back of the room, presumably leading to a more private study rather than the one the Professor held his supervisions in. Despite its diminutive size, the Oakley's room was rammed full with books. The Doctor felt that finding any missing book would be like finding a needle in a very beautifully furnished haystack. He took out the sonic screwdriver to scan for the whispering books but no sooner had the Doctor found it in his pocket, he stopped.

Sat in the middle of Oakley's desk was a solitary library book with a piece of cream paper on top. The Doctor picked up the paper and opened it to find a handwritten note.

"Doctor, thought that you might be coming back for this. Happy reading! Without wax, G."

The Doctor turned the paper over. Perfectly normal except that the handwriting was beautiful and nothing like the Doctor had ever seen before. The Doctor walked back towards Oakley's door and read the inscription on the front.

_Prof. G.O. Oakley_

So the note was from Oakley then. The Doctor walked back in the room towards the book, still puzzling over the note, his mind running too fast for its own good. How did Oakley know that he was coming back? How did Oakley know who he was? How did Oakley know what was looking for? And what on earth did 'without wax' mean? Had he met Oakley before?

The Doctor picked up the library book from the desk and found that at least some of his questions were answered. Below the book was another note which simply read

"Timey-wimey"

The Doctor picked up the second note and shoved it into his pocket along with the first. He would find out exactly who Oakley was when he got back to the TARDIS. Providing that she didn't class Oakley as a spoiler and bar the Doctor access to his own records. The Doctor hated it when the TARDIS developed either a conscious or a sense of mystique.

Just as Thomas had done earlier that day, the Doctor began to feel uneasy in Oakley's room. He turned on his heel and made is way down the stairs taking them two at a time and taking care to shuffle past the cleaner and make as swift an exit as possible before she tried to start a conversation. In time to come, the Doctor would wish that he had spent a little longer in that room.

The Doctor walked briskly across First Court back towards the main gate. One of the porters tipped his hat at the Doctor as he passed and the Doctor returned it with a slight, curt nod before sweeping out onto Trinity Street. The Doctor turned and walked towards the TARDIS, thumbing through the book in his hands. It wasn't yet whispering, nor had it lost any of the words on its pages. It was entirely intact. But it was from the right section of the library and it had been next to Oakley's other whispering books. The Doctor hadn't quite worked out if the whispering was infectious yet. The Doctor snapped his fingers as he approached the TARDIS, the doors opened and the Doctor stepped through, completely unnoticed to the rest of the world. Or so the he thought.

Across the street, a figure had been leaning against the wall by the Round Church, staring at the TARDIS.

"I still can't see what you're looking at" said the Big Issue seller stood next to the figure "Are you going to help me out and buy one of these or not. You've been stood here for ages. Whoever you're waiting for isn't coming, so you may as well keep yourself entertained. They're only £2.50 and you'll feel better knowing you've done a good turn today"

The figure thrust a hand into their pocket and pulled out some money and exchanged it for a magazine

"You're very good. Thank you. Hope you're not waiting too much longer for your mate to come a long" the seller said

"No more waiting. They're already here. And they certainly aren't my friend" the figure said. They picked up their bike that had been resting on the wall next to them and cycled down Bridge Street towards the river.

Inside the TARDIS the Doctor placed Oakley's remaining book on the console and began his scan. He walked up the stairs and took a seat in his leather chair, pulling out the two notes from Oakley. The Doctor scanned the shelf of the books with his notes in. He found the book with entries under 'O'. The Doctor very rarely looked people up in his own records. He preferred to rely on his memory and more than once he thought of completely stopping the practice of taking meticulous notes. Today he was extraordinarily glad that he kept going.

The Doctor found the 'Oa' and ran his finger down the page. But no Oakley appeared. There was no-one that he had met with that name. Or at least, no-one that he had met and recorded. He put the book down on the metal floor and found the book with 'G'. But as soon as he opened the first page he realised that this was a pointless exercise. He knew nothing else other than that the professor's name began with a G. The Doctor now wished, much to his own surprise, that he had spent a little more time talking to the cleaner and actually ascertaining what Oakley's first name was. The Doctor let out a frustrated sigh. Oakley was obviously a spoiler them. He hadn't met him. The Doctor could do without this. Just one day, the universe would be kind to him and he would meet people in the correct order.

The scanner below alerted the Doctor that it had finished its task. The scan on his original book had been inconclusive, but with two books there was less margin for error. He now knew that he wasn't looking for anything alien, but instead something from Earth which really narrowed things down.

The Doctor grabbed the monitor by the handles and swung it round to face him. The Doctor read what was on the screen and then gave it a rough shake. There had to be an error. That couldn't be it.

_'__Lire'_

No wonder it wasn't showing up as alien. It most definitely wasn't. But it wasn't of this time. Lire software wasn't meant to exist for at least another one thousand five hundred years at the least so what was it doing in 2015 in one of the oldest universities in the world?

The Doctor scratched his head and ran another scan on the book. This time he knew what he was looking for. The result came much quicker this time around and the Doctor's suspicions had been confirmed. There was a bug in the software. Instead of the words staying on the pages and merely the sound entering people's minds, the ink was too. These books were literally drowning people in knowledge.

Adjusting the settings on his sonic screwdriver the Doctor realised that he had a lot of work ahead of him. Who knew how many books had this software in and how many of those had bugs. But what was more important was finding out who had dumped the books here in the first place. The Doctor could maybe understand if this was a relic from the Earth's past that seemed to hang around but these books with this very specific, very advanced software, had definitely been placed here by someone which meant that someone else had the capacity to time travel. The Doctor dared not hope that it was another Time Lord but he knew that it couldn't be. To start with he was pretty sure that Gallifrey was gone, despite the Missy's taunts. The second was that this broke all of the Time Lord's principal laws and the only person with a brass enough neck to do that was the Doctor and this certainly wasn't the work of Missy. This was far too subtle.

The Doctor gave the book a quick blast with the sonic screwdriver and the bug resolved itself. Now he just needed to do that on a massive scale. He also needed to get to Thomas, fast. These books had obviously latched onto Thomas in some way and as a naturally inquisitive person, Lire would recognise that Thomas wanted to learn and it would try and help him do just that. The Doctor ran out of the TARDIS. Thomas' introduction to his beloved ship would have to wait.

From the way that Thomas was cycling that narrowed the number of possible colleges down by a considerable amount. The Doctor ran towards the bridge and the first college that he could see that would fit with Thomas' route.

"Please" the Doctor murmured to himself "please, just let this work, please let this be the one"

The Doctor turned into the College and into the porter's lodge. Yanking the door open the Doctor jumped up the two steps into the small room. A sleepy looking porter was stood behind the desk. He had an air of being quite lazy, but really rather accommodating. The Doctor suspected that he wasn't paid well.

"Does Thomas go here" the Doctor asked

"Thomas who?" said the porter "Couple of Thomas' come here"

The Doctor suddenly realised that he didn't know Thomas' surname. He'd have to rely on descriptions

"Thomas, he's tall, skinny, glasses, black hair" the Doctor was getting desperate

"Oh, Thomas O'Mara. You're not the only one looking for him today" said the porter, a tone of suspicion now evident in his voice "Are you one of the UNIT lot?"

"Yes. No. I'm not sure. Where is his room?" the Doctor replied

"G2, just through first court and into second. There is a staircase on your left. Take that up and you can't miss it" the porter said, leaning back in his chair

"Thanks!" the Doctor shouted as he sped out of the porter's lodge. The porter rolled his eyes. These academics got more and more eccentric as time went on.

The Doctor was halfway across First Court when what the porter said suddenly registered. UNIT? The Doctor slowed down his run and walked back to the porter's lodge.

"I'm sorry, you said UNIT?"

**Thanks for reading so far! I've blocked out the rest of the series and have decided upon the titles of the next five stories with Thomas in; The Library of Alexandria, Twisted Reflection, Castle Chance, Heart of a Dog, and Sherlock and the Doctor. **


	6. Chapter 6

**Thanks again to those favourites and follows and those of you who keep reading along. I hope that you are enjoying it so far. Special thanks for the reviews from The Wizard's Daughter, bored411 and woodyt. Have great days, A. **

Thomas' legs were still burning from his cycle back to his room. He wanted to find his library book and get back to the Doctor as quickly as possible. As a consequence, the journey between the library and college was perhaps the fastest that Thomas had ever cycled. The wind had picked up once more and Thomas' cycle had been accompanied by rolling thunder the bolts of lightning whilst the wind was ripping through his hair. The sky was definitely more black than usual for a storm.

Thomas had always loved storms, ever since he was a young boy. As a child he would like to run at the beginning of storms, getting in just before the rain started. He pretended that he was running from the lightning, dodging bolts coming down from the sky. That is how Thomas liked to remember his childhood, a time of innocence when the only real danger was potentially getting rained on after a miss timed run. But Thomas' view of his own childhood was one that was taken through the perspective of some heavily rose tinted glasses. As if to remind him of this very fact, Thomas had rode through a patch of loose gravel on the road and the black flecks flew up to hit his face. For once in his life he was very glad that he wore glasses. At least they shielded his eyes.

Now back in his room, Thomas' search was beginning to feel futile. _Land Degradation and Society_ had not been in the place that Thomas was expecting it to be. After going through the only areas of the room that the book could possibly be Thomas was sure that someone had been in his room. The remaining library books were in a slightly different order and he was sure that the books on his top shelf had been handled by someone other than him. Thomas' thoughts drifted to the porter who inspected his room. Maybe it was him? If he had taken the book then the porter could be in very real danger.

Thomas left his room and took a sharp turn onto the stairs. He was about to start bounding down them when he was stopped by Harley coming up the narrow stairway.

"Are you alright Thomas?" Harley asked, edging past him to the top of the stairs "Did that blonde woman finally find you?"

Thomas suddenly realised that he had not seen any of the small huddle of people that had been stood at the Porter's Lodge earlier that day. He glanced past Harley's shoulder to look out the latticed window. The coast was still clear. It seemed like a lifetime had passed since he was last looking for that little group but it had only been mere hours.

"No. I haven't spoken to them yet. Not sure I want to. Have you?" Thomas asked Harley, taking of his glasses and giving them a quick clean on the bottom of his t-shirt. Harley took off her sunglasses and hooked them onto the top of her t-shirt.

"They just wanted to know where I was. They had a search of my room as well. Not sure why. One of them quite liked some of my latest drawings which is always nice to hear. I thought I'd finally been busted for smoking in there but apparently not!" Harley shrugged her shoulders "Anyway O'Mara, you never answered the question. What's up with you?"

Thomas didn't know where to begin.

"I've lost a book" he said. That was all he could possibly manage at this point. Harley burst out laughing.

"You've lost a book? That's it?! Does it have a huge late fine or something?" Harley was still smiling, but her grin faded when she saw that Thomas was serious "Come on, I'll help you find it. In your room was it?"

Harley grabbed Thomas arm and hauled him back up the stairs. She unlocked her room and hurled her rucksack in before turning back to Thomas.

"We won't find it" said Thomas "Its definitely not in there" he desperately wanted to get back to the Doctor but Harley wouldn't let the subject drop.

"Men are hopeless at finding things. It will take me ten seconds, I swear" Harley looked at Thomas in earnest "Let me help you out. Plus I'd really like to see your room. I've always wondered what it looks like.

"It looks like the inside of my head. All the best bedrooms should look like the inside of their occupants head. Its what makes them unique" Thomas said, unlocking his door and letting Harley walk into his room.

Harley stood in the middle of the room, mouth open slightly and staring. It was beautiful. Stacks and stacks of books. A little library. The smell of old books filled the room but it was in no way unpleasant. Instead it was comforting, almost homely. It reminded Harley of her own childhood home which was covered in books. She would do anything just to have one free day where she didn't have anything else to do and she could just pick a book, any book and it didn't have to be related to her studies, and sit and do nothing but read. It would be bliss. Maybe after the exams.

"I can see why you might have difficulty finding one particular book in here" Harley said "Have you read them all?"

Thomas nodded, a little shyly.

"Its called _Land Degradation and Society" _Thomas said

"Whats that got to do with studying-" Harley asked but was cut off by Thomas giving her a section of the room to look through.

Harley began to read the spines of the books in her section, amazed by the breadth of Thomas' reading but more so by the fact that he had actually read all these books. Harley knew that Thomas would not lie about something like that. Although he was quiet, she knew that he was proud of his intellectual ability and in his own quiet way a bit of a show-off. The constant correcting of those who were wrong was partly why, in her opinion, Thomas struggled to make friends. But she knew that Thomas' corrections were in no way malicious. He merely wanted people to have their facts right as much for their own benefit as for anyone else's.

After ten minutes squinting, Harley announced that she should probably go and pick up her reading glasses which she had left in her rucksack.

"I didn't know you wore glasses" Thomas said, looking up from where he was sat on the floor, double checking another pile that he had already looked through.

"You've never seen me work before have you?" Harley replied

"No" Thomas said

"Not sure how we've managed that" Harley rapped her knuckles on the shelf above the bed.

"Why do you do that?" Thomas pointed to Harley's hand where it now rested on the shelf

"Do what?" Harley said, looking about her

"The knocking. Whenever you leave a room. I may not have seen you work but I have seen you do that" Thomas stood up now, hands on his hips

"Oh. Something I picked up from home I guess" Harley said, shrugging and inspecting her hand "Don't even notice I'm doing it"

"Look, Harley. We really aren't going to find this book. I know it isn't in here, but thanks for your help anyway" Thomas said. He had decided that he should go and find the Doctor and his blue box sooner rather than later. He didn't want to find that the Doctor had changed his mind about him and he couldn't find him. Harley smiled and said anytime that Thomas needed help, just to knock and ask. She left Thomas' room but cast a glance back to see the extraordinary space, crammed with books and the extraordinary boy stood in the middle of it all.

When Harley had gone and Thomas triple checked the pile of University Library books. _Land Degradation and Society_ definitely wasn't there. Thomas couldn't really remember why he had chosen to read that particular book, especially as it was causing so many problems now. It wasn't even a very good book.

Thomas opened his door and immediately tripped over something on the floor. He fell onto the window sill opposite. Thomas looked up to see a figure, clad all in black, watching him from across the courtyard. They looked familiar. Thomas squinted to try and get a better look through the old, poor quality glass but it was no good. He couldn't get a clear picture.

Thomas pushed himself up and turned to look at what he had fallen over. It was a copy of _Meteorology Today_. Thomas' heart sunk when he saw that it had a University Library sticker on the front of it. Nervously he nudged it with his foot. Nothing happened. He crouched down to see if he could hear anything. But the book was completely silent. More cautiously still, Thomas reached out and opened the book. The pages were blank. Thomas stood bolt upright. He spun round to see the figure in black still watching him.

There was a flickering sound behind Thomas, like someone was shuffling a rather large pile of papers. But before Thomas could react, a column of paper had risen up and encircled him, the pages rotating as they did, slicing into his bare arms and face. Thomas raised his arms to protect himself but it was no use. He couldn't move. He was trapped. But though the white storm of pages, Thomas saw the figure in black walk away. Thomas cried out but it was no good. He was sure that his voice was being drowned out by the flurry of papers. The Doctor said the pages weren't dangerous. Didn't he?

It was at this point that Thomas learnt his first real lesson about the Doctor. The Doctor lies.

—

The Doctor was being led by the porter down a narrow, wooden panelled corridor. The wood had been stained black, evidently a long time ago, and the worn stone floor indicated that this was a part of the college that no one really cared for any longer. It twisted and turned, windowless throughout, leaving the Doctor's sense of orientation somewhat confused. The dull hum of the lighting overhead and the clicking of the Doctor and the porter's shoes were the only sounds. The roar of the road outside and the chatter of the students within the college was completely void. If the Doctor didn't know better, he would have said he was underground.

The porter didn't try to make conversation withe the Doctor, instead he kept two steps in-front of him, a large ring of keys in one hand. His pace was quick but he exuded an air of calm.

The floor underfoot began to slope up slightly and the Doctor could see a single door at the end of the corridor. It had six locks. The porter began to unlock the door, taking his time as he hid. The Doctor kept back a respectful distance. The porter opened the door and motioned for the Doctor to pass through. He still hadn't said a word. The Doctor gave the porter a curt nod as he passed. He could see a figure walking towards him, slowly and assuredly. The door behind the Doctor shut hard and he could hear the locks turning.

The room in which the Doctor was dimly lit but as far as he could tell it was relatively small. It seemed the only occupants were himself and the figure.

"Could you get the lights please? The switch is just behind you to your left" the voice was soft and the Doctor felt sure that he had heard it somewhere before. The Doctor took out his sonic screwdriver and depressed the button on the side. The room was illuminated and so was the figure "Of course. Why would you need a switch. I hope you got my note Doctor"

The Doctor was stood, staring at the sad, smiling face of Professor Oakley. The room was small and like the corridor was panelled with wood only this time the colour was a muted green. On each of the wooden panels was a portrait. The Doctor presumed that they were old masters or fellows of the college. It appeared that the only entrance and exit to the room was the one that the Doctor had just used.

"Do you work for UNIT?" the Doctor asked

"Yes. No. I'm not sure" Oakley replied and the Doctor looked startled "They have pretty much rigged all the public areas of the college, Doctor. After all, there is a dangerous person residing within these walls"

"What do you mean dangerous?" the Doctor asked, more curiously this time. Oakley turned on his heel and walked towards the portrait on the far left corner of the room. He pressed lightly on the panel and it came slightly away from the wall. It was a concealed door. Oakley disappeared through it and the Doctor followed.

As Oakley walked ahead, the Doctor was trying his best to work out who exactly Oakley was to him. The professor's black curly hair was peppered with flecks of grey. There was almost something familiar about his walk but the Doctor couldn't quite place his finger on what it was.

"Sorry but who are you?" the Doctor's curiosity got the better of him. Oakley turned around and smiled at the Doctor

"You always were inquisitive. Always asking questions. I'm glad to see that you haven't stopped" Oakley turned around once more and led the Doctor down a small flight of stairs "He's here Kate"

Oakley had led the Doctor to a vaulted room. Stone pillars ran the length of the space and along the walls were stacked bottles wine. Throughout the room glass desks were occupied by UNIT agents, working silently on laptops. Walking cooly towards the Doctor and Oakley was Kate Lethbridge-Stewart. Her cropped blond hair stood out in the dimly lit room.

"Doctor, how very nice to see you. We've found you a desk" Kate motioned to an empty space just to the left of the Doctor. Sure enough there was a desk with a laptop set up with the login name 'The Doctor' "Sorry about the surroundings but we had to improvise"

"What are you doing here?" the Doctor asked

"Probably the same thing as what you are doing. Trying to work out why a porter was found drowned in ink outside two student's rooms earlier today. We've been monitoring this area for a while, on the advice of Professor Oakley here. I believe you are old acquaintances?" Kate said. The Doctor looked confused. He opened his mouth to speak but was beaten to it by Oakley

"I think its a little more complicated than old acquaintances, Kate" Oakley said, giving the Doctor a glance whose expression he was really struggling to read

"Ah" said Kate "Timey-wimey?"

"Something like that" said Oakley "If you'll excuse me, I need to get back to my desk. Call me if you need me. Pleasure to see you again Doctor"

Oakley then did something very odd. He bowed. This time the Doctor didn't even try to hide the sheer confusion that he was feeling. Oakley however didn't seem to register this. He straightened his back and walked away towards his desk where he sat down and began to work. But he kept an eye on the Doctor.

"Kate, there is something wrong with the books. The technology embedded within them is far too advanced for the twenty-first century" the Doctor said, turning towards his desk and taking a seat. He took a moment to appreciate the frosted glass and swivelled on his chair slightly before logging in "What's my password?" he asked Kate

"Theta" Kate replied "You said technology?"

The Doctor typed in the password and pressed enter. The UNIT desktop appeared and the Doctor began to browse their catalogue of recorded alien technology.

"Yes. Its not alien though. Its human. Just out of its time. I'm just checking that you haven't come across it before and mis-categorised it. You know what humans are like Kate, always making mistakes. Its no wonder, their tiny little brains get clogged up so easily" Kate looked impassively at the Doctor. Following years of working with him she had grown used to his attitude towards humanity. But deep down, she knew that he cared. Otherwise, why else would he keep coming back?

"No. There is no record. This is definitely new. Which leaves us with two questions" said the Doctor, scratching his head. He'd throughly searched the archives and nothing had been recorded of the Lire previous to the current date.

"The first is surely going to be how we stop them, which I presume is going to be the hardest one" Kate replied, motioning over to Oakley to come forward.

"Actually, thats just where you are wrong. Stopping them is easy. The second question is the hardest one. Its who brought them here" the Doctor said as Oakley re-joined the pair. The Doctor turned to address Oakley "You knew I was looking for the books, how?"

"I'd noticed something was wrong a while ago. I alerted UNIT" Oakley said, somewhat dismissively "Occasionally there are problems related to alien lifeforms and technology that you aren't here to deal with. It does happen. And when those problems occur, there is a whole team of people who act as UNIT's eyes and ears on the ground. I am merely one set of those"

The Doctor had the feeling that Oakley wasn't 'merely' anything of the sort.

"A friend of mine has an affected book in their room. They've just gone to get it" the Doctor said "I said I'd meet him at the TARDIS but change of plan. I'm here. I need to go and get him"

"What's his name?" asked Kate "If the book has been in his possession for a while he may be in trouble"

"Thomas" the Doctor replied "Come to think of it I don't know is second name. Not that it really matters" the Doctor smiled. But Kate and Oakley were unsmiling. The two were exchanging anxious looks.

"We'll come with you" said Kate, her voice had a cold but concerned edge to it.

—

Harley could hear a flickering sound outside the door, like someone was shuffling hundreds and hundreds of piles of paper simultaneously. She looked up from her work and frowned. Placing her drawings carefully to one side, she stood up awkwardly as a shot of pain travelled up her left arm. She mentally berated herself for leaning on it again. Harley tapped her trouser pocket to check she had her card to get back into her room. She opened her door a crack and looked out.

The noise of shuffling paper intensified and to her right Harley could see what looked like a column of paper revolving in the middle of the corridor, just outside Thomas O'Mara's door. She threw her door open and stepped out into the corridor, squarely facing the whirl of paper.

The column began to move as if someone was thrashing around in it. Harley squinted and realised that there was, indeed, a person, trapped in the paper. It was Thomas. Harley felt a little sick as she noticed that the paper spinning around him was not a bright white but was instead flecked with red. It was blood. It had to be.

Harley had to work out how to stop this. She could work out why there was a vortex of paper surrounding her neighbour at a later date. For now, she just had to get a grip. Outside, another bolt of lightning tore through the sky, followed by a low roll of thunder. The storm was definitely getting closer. Surely it was almost on top of them now. Harley silently cursed the storm for interrupting her thought process but then she stopped. Storms. That was it. She ran to the window to see if it was raining. Unfortunately it wasn't. There was only one thing for it. Harley darted back into her room, propping the door as she went. She could just hear Thomas shouting over the revolving paper.

Harley went to her desk and found the blue recycling bin underneath. She emptied the contents out onto the floor. And jogged over to her bathroom. She placed the bin in the shower and turned on the water. Slowly the bin began to fill up. Harley went back into the corridor and shouted to Thomas to hang on. It was no point explaining what she was going to do. She doubted that he would hear it anyway.

Harley went back into her bathroom and saw that the bin was almost full. She turned off the shower and gritted her teeth. She picked up the bin and lifted it onto her right shoulder. Despite her twisted left side and all the scars, Harley was in very good physical shape. She was stronger than she looked. Harley walked slowly back into the corridor, careful not to spill the water as she went. Now was the difficult part. She would need to use her left arm. Harley hoisted the bin above her head and with a shout poured the bin's contents on Thomas and the paper. Immediately the paper stopped. It had lost its structural integrity.

Harley gave a small smile as the paper began fall away from Thomas. Once she was sure that the paper had lost whatever kinetic energy it had, she threw the bin to one side, loose paper floating down around her and the figure of Thomas on the floor who was now sat in a very wet heap on the floor. Thomas had an air of semi-permanent artful begdragglement as it was but this certainly wasn't part of his 'look'.

"What was that?" Thomas asked, gasping for breath and inspecting his arms which were now covered in tiny red lines and stinging from the water that Harley had deployed to stop the paper.

Harley bent down and picked up a sodden blue and white cover with a snow covered tree on the front.

"I believe it was Ahren's Meterology. Over 1000 pages. Nasty" Harley pulled a face and threw the cover back down on the floor and kicked it to the side of the corridor next to the bin.

"How do you know it has over a thousand pages?" Thomas asked, looking up at Harley now genuinely curious.

"Look around you Thomas" Harley said sarcastically, motioning at the large mound of paper that Thomas was currently sprawled in "Also I have read it"

"But you aren't studying Geography" Thomas countered

"No. You're not studying theology or philosophy or English yet you walked through the court yesterday with your head in a copy of The Snark" Thomas said nothing but squinted at Harley "I needed it to understand hurricanes. We have a module on designing buildings to withstand them and other natural disasters. I just wanted to know a bit more about it"

"So this was your book?" Thomas asked, eyeing Harley suspiciously

"No, I gave my copy back months ago. Anyway, why are you asking that, it was in your room wasn't it?" Harley said

"No it wasn't. It was in the corridor when I left my room. You didn't put it there then?" Thomas said

"No I didn't" Harley replied, looking around her "I didn't hear anyone else come up the stairs either. Once again O'Mara, why do I get the feeling that one of us is lying?"


	7. Chapter 7

**Evening all! Same spiel at the beginning as usual. Thanks for the follows, favourites and reading along this far! Special thanks for the reviews from Uzumaki Rin, bored411 and SlytherinHolmes. Happy reading y'all! **

The Doctor and his entourage walked back through the windowless corridor through which the porter had led him.

"So how long do you intend to be lurking in a wine cellar Kate?" the Doctor asked as his companions struggled to keep with his brisk pace.

"Not too long, I hope. We've got a good idea of who is behind these attacks but as you said, how or why this is happening remains a mystery" Kate replied in her usual blunt tone, although her attitude towards the Doctor was far from unfriendly.

"What are your suspicions, Doctor?" Oakley cut in, his voice as soft as ever

"Its malfunctioning tech, it nearly always is nowadays it seems. What is worrying me is that there is someone, or something, with the ability to travel into the future, select this piece of software, bring it back to the twenty-first century, perhaps even earlier, and successfully install it in a load of Geography textbooks. If they wanted world domination, using Geography books is not the way to go. Surely you'd pick a more popular subject?" at the end of the Doctor's speech, Kate stopped abruptly in the middle of the corridor.

"I'm sorry" she said, trying to piece together this increasingly complex puzzle in her already overworked mind "but Geography books?"

"Yes" said the Doctor, spinning round to face Kate "Haven't you noticed their all Geography books. Or to be more accurate, their from that section of the library specifically"

"But there are some that are economics, politics -" Kate began but she was stopped by the Doctor throwing up his arms in an overly dramatic move that did nothing to hide the irritation that he was beginning to feel

"Oh you people! Geography is a very broad subject, perhaps the broadest in the universe. At a university level particularly. Had I the misfortune to go to university on Earth, I probably would have studied Geography. Takes the best bits from all the other subjects and puts them together in a lovely little package" the Doctor mimed tying a bow on top of an invisible package as he spoke and flashed Kate a winning grin when he had finished, slightly cocking his head to one side as if to challenge her to ask any more inane questions.

Meanwhile, Oakley had continued to walk ahead, seemingly unconcerned, or maybe just uninterested, by what the Doctor had to say. As he walked he tapped his left hand along the wood panelled walls. The small silver ring on his left hand made a pleasing sound as it connected with the wood. When the Doctor had walked into his office earlier that morning, that was the first thing that he noticed about him. The Doctor's own ring was larger and gold but it was unmistakable who it belonged to. It was because of this thin band of metal that Oakley had recognised the Time Lord before he had even looked at his face. Oakley had initially been irritated, possibly even upset, that the Doctor had failed to recognise him. But people change. Who knew how old the Doctor was and Oakley knew that he himself looked very different to the last time that he had seen the Doctor. As the day wore on, Oakley began to realise that his anonymity in the eyes of the Doctor could well be an advantage. In fact, it definitely was an advantage. But that did not mean that he would not push the bounds as close to recognition as he possibly could.

By now Oakley could hear that the Doctor and Kate had resumed their brisk walking pace, still talking to each other discussing the finer points of something that was rapidly becoming less and less interesting to the Professor. Oakley emerged from the passageway ahead of his companions and nodded at the porter who was keeping guard of the door. Oakley knew where he was heading. With an almost uncharacteristic determination, he strode across first court and into second. He stopped at the edge of the court and looked up to a small latticed window just to the left of the building in-front of him. What he saw made him freeze. Once the shock at what he was seeing had dissipated, he smiled. It was only small. But it was defiantly a smile. Anyone who worked with Oakley would be as surprised at this small indication of emotion as Oakley had been at Thomas' outburst of speech earlier in the day. For a brief moment, the imperceptible sadness had left the man's blue eyes.

—

Thomas pushed himself up onto his feet with as much grace as he could manage. Someone definitely had something against him. Harley's twisted figure was still stood in the centre of the corridor. Thomas took his glasses off and wiped them clear. Someone needed to invent water repellent glasses.

Harley had begun to talk about calling maintenance to come and dry out the corridor when she stopped mid-sentence and did a double-take. She had spotted something out the window.

"Is it the man in black?" Thomas asked, still pulling off sodden pages that were stuck to his person "I saw him before"

Harley didn't turn to Thomas but continued to stare out the window.

"Is this what killed Steve? The flying pages of a book?" Harley's voice was hardly above a whisper and she had taken on an almost deathly pallor. Although Thomas could only see the right side of her face, he was sure that even the scarred left side would have taken on his unhealthy colour.

"Sorry, Steve?" Thomas asked, moving slowly towards the window in-front of him whilst keeping an eye on Harley

"The porter who died outside your door" Harley turned to look at Thomas who was now looking completely lost. Her green eye locked onto his and Thomas felt the urge to tear his gaze away. But he couldn't. Something was stopping him "A porter was found dead outside your door this morning. Thats what they want to question us about. His death was described to me as 'unexplained' but the questions were about books. Well the ones that stretched beyond the usual where were you at x hour ones. And now you've been attacked by a revolving column of loose pages. So, frankly Thomas, I would like to know what is going on an why whatever is happening is particularly attracted to this corridor in particular"

Harley's voice never lifted above a whisper. It scared Thomas far more than if she had stood over him and bellowed. Her stillness, her absolute calm in the face of chaos was terrifying. Thomas managed to rip his gaze away from Harley and stood in-front of the window. His hands were gripping the sill so tightly that his knuckles had turned a bright white. He needed to slow his thoughts down. He needed to pick out what was essential and try and work himself out of the hideous situation that he suddenly realised that he was in. The figure in black was no-longer in the court but instead Thomas could see Oakley standing by the main archway between first and second court.

It was no wonder that Oakley was treating him with a higher degree of suspicion that usual. A dead man had been found outside his door. Thomas supposed that that was what the text in the supervision was about. Oakley had wanted Thomas to confide in him and tell the Professor about what, supposedly, he had done. Oakley was offering him a route out of a maze that Thomas was unaware that he was even in. Thomas heart sank when he saw the Doctor and the tall blonde woman who had been looking for him coming up behind Oakley. Did the Doctor suspect him? Was this really all over before it had even begun? Whatever it was.

Thomas let go a deep breath that he didn't even realise that he was holding. His voice was much more gravelly and quiet than Thomas would like it to be. He wanted to sound braver than he felt. He wasn't sure it was working.

"Harley, you have to believe me. Whatever is going on here, whatever Oakley and that woman think I did, I didn't do it. I am just as lost, just as confused as you are. Please, please believe me on this" Thomas twisted his torso around and looked pleadingly at Harley. But Harley was still looking past him and out the window, apparently at the small huddle of people now stood in the archway. She remained silent and Thomas turned back to the window and began inspecting his bare arms that were peppered with paper-cuts.

"You know what, Thomas? I believe you" Thomas spun round to look at Harley again, quick enough to see her quickly place something in her trouser pocket. He was about to ask what it was when she spoke again "Who is Oakley?"

Thomas smiled. Harley was on his side. Uncharacteristically he reached out and took her hand. Their hands fitted awkwardly together as even on her better right side, two of Harley's finger's curled in towards her palms. Thomas gave her hand a quick squeeze and led her towards the spiral staircase.

"Oakley is mine and Ezekiel's main supervisor for our module on time. Or rather theories about how time works" Thomas said "We need to get to the Doctor though. I haven't known him long but I'm sure he can help"

Harley was giving Thomas an unreadable look which flitted somewhere between incredulity, fear and surprise. As Thomas reached the bottom couple of stairs he felt that Harley was becoming a dead weight at the end of his arm. She seemed to be resisting him somehow. Thomas assumed that her surprise and whatever else it was she was feeling was driven by a combination of factors including the fact that this was the most that she had ever heard him speak but also that his voice was betraying the sense of awe he had for the Doctor. He sounded like he couldn't believe his luck. Which was true. Despite all that was going on around him, he felt like the luckiest man alive. There was some small part of him that wondered if this was wrong. Harley opened her mouth to say something but closed it again.

"Come on, I'll introduce you" Thomas said as the two descended the stone stairs towards First Court. As they left the building Harley looked up and saw that the sky had got even darker. It looked like it was threatening to rain. The storm was about to break. Thomas dropped Harley's hand and began to stride towards the Doctor, Oakley and Kate. He was walking at a quick pace but Harley seemed more reluctant. Thomas was beginning to get frustrated and was about to turn around and usher her on but he stopped himself, suddenly realising that as strong as she may be, maybe she was walking slower because she couldn't walk any faster. Her twisted arm and turned in fingers might not be the extent of her physical impairment. Despite his urgency to get to the Doctor, Thomas slowed down.

Even in the imperceptibly short time that the pair had been outside, the sky had darkened again. The clouds were no longer a dark grey; they were almost black. Thomas shuddered slightly and Harley was looking particularly wary, her one good eye darting up to the sky. The Doctor was now talking animatedly to both Oakley and Kate. His lean figure was bounding along the path towards Thomas and Harley with a distinctive walk that Thomas would come to recognise from great distances. Thomas raised his hand slightly to greet the trio and turned to Harley.

"That's him. The Doctor. The tall one and Oakley's next to him" Thomas said, gesturing towards the older men.

"Yeah" Harley said quietly "I recognise him now"

Suddenly there was a clap of thunder that seemed to bounce off the walls of the College, reverberating around the court. Thomas and Harley both looked up, their heads jerking back almost painfully. Small, grey droplets began to descend from the sky. There was a flash and another low growl and the rain intensified. The Doctor, Oakley and Kate turned and ran back to the shelter of the College gateway. Thomas and Harley followed them.

As Thomas and Harley drew up into the archway, Thomas took his glasses off to clean them again.

"They really need to invent glasses that are both rain repellent. That's the second time I've thought that today" Thomas shouted over the now pelting rain

"They have" replied Harley

"Well, in that case, rain repellent and affordable" said Thomas, still working to clear off the water from his glasses which seemed to be tinged slightly grey. As he worked he realised that throughout their dash to the archway, Harley had kept pace with him. In his rush to get out of the rain he had forgotten his gentlemanly consideration and ran at full pelt after the Doctor, Kate and Oakley. Thomas was a fair runner and keeping up with him had been a challenge for his classmates back home. If Harley was perfectly able to move quickly, and Thomas also noticed, with incredible ease as she was neither out of breath or unable to hold a conversation whilst running, then why was she walking so slowly before? Thomas brushed the water from his arms as his cuts were beginning to sting again.

"What did they do to you?" Oakley said with a genuine concern and sorrow that took Thomas aback. But before he could answer the Doctor let out a shout. Thomas put his glasses back on and the world came back into focus. The blonde woman was casting a very confused look at Oakley. The Doctor seemed oblivious and thumped his head with the palm of his hand.

"Oh I'm getting old! It's not just about how they kill you; it's what they do to you before!" the Doctor looked almost crazed, his eyes wide and excited "Come on! Think! What do they do to you before? Thomas, you're smart. Come on! The books what do they do?"

Thomas looked slightly embarrassed to be singled out, but also a little proud.

"They whisper" he said

"Good. What do they whisper?" the Doctor nodded

"They whisper... what's in the book" Thomas said, his confidence building "Wait, they're reading out the book!"

"They're not just reading it, Thomas. They're teaching it" said the Doctor, oblivious to anyone else but him and Thomas. Meanwhile, Oakley had been reaching out for Harley, but she'd begun to back away, her eye darting between the Doctor and the Professor. Kate was reaching for Oakley, trying to diffuse whatever it was that was going on.

"Its something called Lire. A piece of software. The fact that its in a university is not surprising at all. The fact that its gone a bit rouge and is consuming people is. And the fact that its in the twenty-first century even more so. Humans are amazing creatures. But also incredibly lazy. If they can find a quick solution to something then its happy days for them. The same goes for reading. As humanity advanced, so did education. The volume of information that students were required to retain began to become overwhelming. Thomas, if you think your course is tough now, try taking it in five hundred years time. In order to cater for these raised expectations, but mainly to cater for the extraordinary laziness of students, a very bright group of undergraduates, at this very university in-fact, came up with a solution. In 2610 the Lire software was developed. It was, or rather is, a piece of teaching software that takes advantage of very low level telepathic waves that human brains emit but cannot fully control. When turned on, the Lire software tunes into these and latches on. Whatever book that the software is overlain, that content is taught, whispered if you like, directly into the brain. The effects for learning are somewhat limited. It doesn't improve memory necessarily, but the information is fed in and can be stored for just enough time to take a test on the subject. One need only turn on the software in a book, leave it on a table and proceed to play FIFA 610 and still get a decent mark on the mid-term exam the following morning. It was brilliant. It revolutionised learning. You know where the idea stemmed from? The old human idea that if you put a book under a pillow and slept on it, its knowledge would seep into your brain overnight. Who knew! An old wives tale would become the basis of one of the greatest software developments in human history" the Doctor paused briefly for breath. Thomas was enthralled "But its gone wrong. There's a bug in the software. The energy that locked onto low-level telekinesis is being re-directed into kinetic energy. The ink is coming to life and latching onto anyone it can find. Actually thats wrong. Its not just anyone. Its particularly attracted to people who want to learn. To people who are curious. Which is maybe why it has a particularly affinity for you Thomas. All we need to do is de-bug the software. I have the correct new line of code set up on the sonic-screwdriver but the challenge is reaching all the affected books before time runs out. Before this thing mutates any further."

"But you said that this was contained to Geography books. Or rather books that pertained to Geography" Kate said, seeming to have processed this vast amount of information that the Doctor had supplied at incredible speed.

"For now they are. But this thing is clever. Very clever. It will be able to jump between books soon. It may even be able to do it now. But I don't know. I need to get back to the TARDIS. Thomas did you pick up that book?" the Doctor turned to face a somewhat stunned Thomas

"That was brilliant" was all that he could manage to say

"Yes I know" replied the Doctor "But do you have the book?"

"No, it wasn't there" Thomas said, a little apprehensive of the Doctor's reply.

"Was it Land Degradation and Society by any chance?" Kate asked, hands on hips

"Y-yes. Yes it was" Thomas replied

"That was it. That was the book that the porter was reading when he was killed. Or rather when it killed him" Kate said, in a very manner-of-fact tone.

"Well in that case, you are forgiven for not finding it" the Doctor gave Thomas a small nod and he wondered why the older man hadn't yet said anything about his appalling physical condition.

The rain was now torrential and staying. The storm had definitely set in. The rain was defiantly grey. The puddles forming on the rubbed stone floor of the court were a darker grey, mirroring the sky above.

"Doctor" said Kate "The rain…"

The Doctor stuck his hand out into the downpour and brought it back in under the archway. He looked at it for a moment before licking it. Kate pulled a face and Oakley looked slightly amused. Harley's face was like flint. The Doctor pulled a face and wiped his hand on his coat, drying it off.

"Diluted ink. Very very diluted ink" the Doctor turned to face Thomas "Maybe running that stuff down the drain earlier wasn't such a good idea"

Thomas smirked slightly and shook his head. It seemed they were partners in crime.

"Anyway" the Doctor clapped his hands together "Team! Comrades! Gang! To quote scooby doo, we need to split up. Kate, you and Oakley go and try and find out from the tech lot if they can find out if this bug is mutating, if so how fast. Should be pretty simple to do. You don't have to work out why or how to stop it. Just work out the speed and let me know. Send a message on the psychic paper. Thomas. You're coming with me. We need to stop this thing."

The Doctor wiggled his eyebrows and was about to walk off with Thomas when he stopped. Harley was still stood under the archway.

"Sorry, you are?" the Doctor asked. But Harley never answered.

"She can come with us" Oakley said

"Really, I don't want to be any trouble. I have plenty of work to be getting on with" Harley said, somewhat stiffly "I have a project due in this time next week"

Oakley looked at Harley and then turned to Kate, as if expecting her to say something.

"Its OK. You can go" she said to Harley. Clearly this wasn't what Oakley was looking for. He was now looking imploringly at the UNIT leader. Harley gave Kate a small smile of thanks and turned to leave. As she walked away, Thomas noticed that her right hand came to rest on whatever it was that she had stowed away in her pocket earlier. As the Doctor, Thomas, Kate and Oakley dispersed, running to the main porter's lodge and college entrance attempting to dodge the rain, Harley delved her hand into her pocket. Thomas glanced back at her and saw a faint flash of silver as she took the object out and clasped it firmly in her hand. Another low rumble enveloped the college as the twisted, but proud, figure of Harley Lauda walked calmly through the grey rain.


	8. Chapter 8

The Doctor could barely look at Thomas as the pair jogged through the grey rain to the TARDIS. Why was it, that whatever his intentions, the Doctor could never keep his companions from pain. Physical or emotional. OK, he wasn't sure if Thomas was going to be his companion, but right now he was the closest thing to it. And for some reason, that the Doctor still couldn't quite pinpoint, the Doctor wanted to protect him. He had only been with Thomas for a day, but this quiet but sparky, lonely but charming boy had caught his attention.

Clara wandered back into the Doctor's mind again. She was giving him an odd look. Even his own mental version of Clara was 80% eyes and 20% disapproving glances. He preferred it when she was smiling. But he never told her that. The Doctor vaguely thought that he would now never get the chance to. But he shut that particular line of thought down almost as quickly as it appeared. Pining over Clara now would not help.

There was another clap of thunder and the rain intensified once more. The Doctor grimaced and turned up the collar of his coat to try and give him self some protection from the torrent of ink and water. This was not his day.

The face of Oakley swam in-front of him and the Doctor felt like he was going to evaporate with repressed frustration. Just who was he? The Doctor was used to dealing with situations with mystery at one end i.e. the threat. He couldn't cope with mystery at both ends. He liked to know who he was working with. It was obvious that Oakley had recognised him from some sort of long-standing relationship between the pair. Kate said that they were "old acquaintances" and Oakley had bowed to him. Actually bowed. No-one bowed to the Doctor. People had bowed to his parents back on Gallifrey, but not to him.

As the TARDIS came into view, the Doctor remembered that this would be the first time that Thomas would see his beloved ship. No matter how many times the Doctor brought someone new onboard, he enjoyed seeing their reactions. The bright blue of the wooden box cut through the grey rain which was making visibility incredibly poor. The cars on Bridge Street were running a lot slower than usual and many cyclists had given up and were now walking their bikes through the rain on the pavements instead.

The Doctor came to a halt in front of the TARDIS doors and turned to speak to Thomas, locking onto the boy's eyes and refusing to look at the rest of him.

"You're going to love this" he said. Thomas frowned. The Doctor opened his mouth to say something else but on reflection closed it. Instead he pushed on the TARDIS' door and held it open for Thomas to enter. Once he saw that the boy had gone through, the Doctor glanced around the street and followed him in. The Doctor nearly walked into Thomas who was stood in the middle of the walkway to the console, gripping the rail.

The Doctor walked past him and went to stand by the console, his hand resting on a lever.

"You've got questions, I'm sure. But we don't have too much time. So if you could restrict your general wonder, amazement and bafflement to a five minute interlude at most, that really would be much appreciated" the Doctor said, looking at Thomas' face. He looked like Christmas had come early.

"Its…its…." Thomas began. The Doctor knew where this was going. He walked around the console to the screen and tapped something out that Thomas couldn't see. The Doctor looked up again to see if Thomas was still breathing because the boy still hadn't finished his sentence. Thomas was still looking around the TARDIS, gazing upwards towards the domed roof of the console room.

"Its…b-b-beautiful" Thomas eventually managed to get out. The Doctor looked taken aback and was a little disappointed. What happened to the whole 'bigger on the inside' routine? But the Doctor had to agree with Thomas. It really was beautiful although the Doctor rarely regarded it as such. Usually he was in too much of a rush to really appreciate what his craft looked like. To him the TARDIS was beautiful not just because of its stunning interior but because it had transported him throughout the universe. It had protected him and it had guided him. The TARDIS always had his best interests at heart, even if this wasn't particularly evident at the time. She looked after him. And she was his last link to home. Well, his last link to home that wasn't a megalomaniac dressed as Mary Poppins.

"Its a TARDIS. Stands for Time and Relative Dimension in Space. Anywhere, anytime in the universe that you want to go, or occasionally don't want to go, the TARDIS will take you there" the Doctor said, opening his arms in welcome to Thomas as he spoke before dropping them to his side.

Thomas didn't know where to begin. There were plenty of questions to ask. But he had to ask them in the right order.

"Is it alien?" Thomas asked

"Yes" said the Doctor

"Where did you get it?" Thomas said, moving slowly towards the main console.

"My home planet. Gallifrey. They were grown not built. Its not a machine, she's a living thing" the Doctor replied "And before you ask, yes I am alien. Time Lord to be precise"

Thomas nodded. It looked like he was filing that particular piece of information to process at a later date. Thomas reached out to touch the console and the Doctor nodded. Gingerly, Thomas touched the lever closest to him. Without warning, the TARDIS lurched violently to the left, as if to throw Thomas off. The Doctor grabbed onto the console, pulling a row of levers and apparently calming the machine. Thomas looked startled and the Doctor reassured him that he had done nothing wrong and that the TARDIS could occasionally get a bit moody. It was nothing personal. Once Thomas had regained his composure, he spoke up

"Who grew it?" he said

"Sorry?" the Doctor replied, as the screen in-front of him pinged and a small drawer on the console opened. The Doctor pulled out a small glass vial with glowing yellow dots flying about inside it.

"Who grew the TARDIS?" Thomas clarified. The Doctor closed the drawer and wondered where to begin even answering that question. The fact of who grew TARDISes was an uncomfortable piece of Time Lord history, one that was quite personal to the Doctor. For the second time that day, the Doctor's mind wandered back to the gardener's reading room and the view of the field and the oak tree. There was something in the back of the Doctor's mind that he felt wasn't quite connecting, but he couldn't put his finger on exactly what it was. His right hand drifted back to his ring.

"There were people specially designated to grow them. It took years and the work was difficult but the results, as you said, were beautiful" the Doctor replied. He decided that his answer was vague enough to conceal the horrific truth but with enough information to satisfy Thomas. It seemed to have worked because Thomas nodded, accepting the older man's answer. The Doctor walked to Thomas, the glowing vial in hand.

"Does that hurt?" the Doctor asked, motioning to Thomas' arms.

"Its alright, I've had worse" Thomas replied. The Doctor winced as he spoke; he didn't even want to consider the implications of that statement. The Doctor was struggling to think of anything more unpleasant than receiving thousands of paper cuts that were then soaked in stinging water.

"Hold out your arms" he said and Thomas did as he said, completely trusting him. The Doctor opened the vial and poured the contents onto Thomas' outstretched, scratched arms. Hundreds of nanogenes spilled out and wizzed around Thomas, working out what they needed to work on. Thomas was stood frozen, his mouth open in awe. He could feel the pain leaving his arms and face and through the yellow light could see that the cuts seemed to be healing themselves. Thomas looked up at the Doctor and started laughing. Thomas couldn't remember the last time that he had laughed, but now seemed like a good time to pick up the habit again.

"They're called nanogenes. Heal you're wounds so you're good as new" the Doctor said, gathering the nonagons back into the vial with a small buzz of the sonic screwdriver.

"That's brilliant" said Thomas, inspecting his newly healed arms. He even saw that the small scar on his right arm had also disappeared.

"Right, to business" the Doctor bounced back to the console screen and deposited the vial in the draw before logging back onto his previous research into the Lire software.

"Just one more question" Thomas said and the Doctor looked up "If you're an alien, why do you have a Scottish accent?"

"Lots of planets have a Scotland" the Doctor replied and Thomas quirked an eyebrow.

—

"How long? Exactly how long have you known?" Oakley spoke with a hushed urgency. Kate looked irritated. She didn't have time for this right now. Frankly she didn't have the time for this at any point but Kate bit her tongue and refrained from telling Oakley exactly what she thought.

"Gideon, please" Kate said "We need to focus on getting out of the mess that we are currently in before we start creating another. Lets just work out the pace of mutation, send it over to the Doctor and then once this is finished, you and I can have a talk about this"

"I am not doing anything, until you tell me exactly what is going on here" Oakley said, his voice still refusing to rise above the level of a whisper. Kate sighed.

"In all honesty, I don't entirely know myself. All I know is that we, as a planet, are pretty vulnerable at the moment and I need your help. Work with me on this, please." Kate said, her harsh tone softening slightly "You don't have anything to worry about. We'll protect you if it comes to it"

Oakley looked heartbroken. Kate looked away from Oakley and busied herself looking for the latest date readout from the technicians. The Professor had taken a seat at the table in the middle of the room. He was inspecting his wedding ring.

"It won't come to it. It never will" Oakley's voice was thick and Kate looked up from her work

"How do you know? How can you be certain" she asked, careful not to push Oakley over the edge that the man was apparently stood at

"I can't be one hundred percent certain" Oakley replied "But the fact that I trust that nothing will happen is what matters. At least to me anyway"

Kate smiled slightly at Oakley and nodded her head. Oakley rubbed his face with his hands and leant back in his chair. After a while he seemed to collect himself and set about helping Kate find the right readout to send to the Doctor. Whatever happened in the future, he needed to make sure that he was above suspicion. He needed Kate's support just as much as she thought that she needed his. Eventually the correct rate of mutation was found and Kate and Oakley parted ways. Kate went to sent the Doctor a message and Oakley headed back to his rooms.

Oakley decided to take the longer back route to his own college. He couldn't face the noise of town and instead wanted the green of the college back's and the gentle flow of the river. Taking a right he headed up towards the crossing and took another left walking towards Queens road. When he got to the path along the backs it was deserted. He was the lone walker in the storm. The grey rain seemed to be intensifying. Oakley cast a concerned look up to the black sky only slightly visible through the verdant green canopy above him.

—

The psychic paper in the Doctor's pocket buzzed slightly and the Doctor pulled it out to see that Kate had sent him a message. The rate of mutation was much greater than the Doctor had hoped for but it was at least manageable. The Doctor entered this new information into the TARDIS' computer. He plugged the sonic screwdriver into the main console and downloaded an updated version of the frequency needed to neutralise the threat that the Lire was posing.

"All we need now is a way of transmitting this to all the affected books, some of which won't be in the library" the Doctor said, scratching his head. Thomas had taken a seat on the chairs next to the console and was propping his head up in his hands, deep in thought.

"Do we have to hit all the books? Because if this is a mutating bug then it takes it form from the last strongest in the chain. If we ensure that the majority of the books are made safe then surely the dominant code will be the safe version. The bug will duplicate the safe version, which presumably has a fail-safe within it preventing any further development" Thomas said, although when he spoke he was addressing the floor rather than the Doctor. This whole talking to people's faces thing whilst maintaining eye contact was a little new to him.

The Doctor stared at Thomas. For once in his very long life, the Doctor was lost for words.


	9. Chapter 9

"I would say that you are a genius Thomas but I'm in the room" the Doctor said, spinning back on his heel to face the console once more "We need to get back to the library. Time for your first flight"

The Doctor pulled down hard on the acceleration lever. As the TARDIS' engines engaged Thomas jumped up from his seat. The sound of the TARDIS' engines made him feel amazing. The Doctor was dashing around the console trying to make the ship's flight as smooth as possible. Despite the Doctor's age, Thomas thought that he was surprisingly agile and able to move quite quickly. Little did Thomas know how new on the Doctor's face was.

The TARDIS rocked wildly as they travelled and Thomas supposed that this was what it would feel like if he were sat on the back of a raging bull.

"Believe it or not Thomas, I am actually in control of this machine!" the Doctor shouted

"I thought you said it was a living thing not a machine" Thomas yelled back, slowly managing to get his balance. The Doctor opened his mouth to reply but closed it again, frowning.

A phone began to ring over the din of the engines. Doctor explained to Thomas in rather terse terms that as he had no more available arms and the TARDIS was being particularly difficult, he would have to answer the phone. Thomas staggered over to the main console. He found that if he treated the floor as a giant skateboard and bent his knees slightly he could balance much better.

The Doctor pushed the console screen around to Thomas and told him to press the symbol in green on the right of the screen. Before Thomas even began to think about commenting on the vast array of circular symbols and writing on the screen the TARDIS jolted again once more, a little more violently this time. Thomas only managed to stay upright by employing a vice like grip on the screen's handle.

"She's not usually this jumpy I swear. You're next ride will be much smoother" the Doctor said as he violently jabbed at an array of buttons that Thomas gawped at. The shrill cry of the phone cut through the TARDIS once more and Thomas finally answered it.

"Hello" he said, somewhat hesitantly

"Is that the Doctor?" the clipped voice of Kate's voice filled the TARDIS

"Is the Doctor and Thomas" Thomas replied

"Where are you going?" Kate asked and then Thomas suddenly realised that he didn't know.

"The University Library" the Doctor cut in "Meet us there at 15:00"

"What day?" Kate said

"The same as we last spoke. Bring copper wire. Many, many reels" the Doctor said, briefly gesturing with his arms before the ship jolted again and threw his hands down onto the console, back to the organised chaos that is flying the TARDIS.

"How much is many?" the exasperation was only thinly veiled in Kate's voice

"157 feet" the Doctor replied, pulling down hard on a bright blue lever. The TARDIS' engines slowed down and the console room stopped jerking around. Thomas stood frozen, gripping metal rail running around the room. Although parts of Thomas, particularly his stomach, were glad that the TARDIS' journey was complete, another part of him wanted to hear the engines start up once more.

"Right" said the Doctor, bounding to the door "We're here"

The Doctor flung the TARDIS doors open and stood outside were Kate, Osgood and a tall UNIT colonel who the Doctor had never seen before.

"You're exactly on time, for once" Kate said, hands in pockets and at least a dozen reels of copper wire at her feet. The wind was picking up again and it looked like the grey rain would start to become heavier again.

"Osgood?" the Doctor asked, edging forward towards the young scientist.

"Yes, I'm alive. I'll explain later" Osgood said offhandedly, waving the conundrum away.

"Is the reason science-y?"

"Something like that" Osgood nodded and the Doctor grinned. He almost looked like he was going to give her a hug but something made him hold back.

"Have you two quite finished?" Kate cut in. "Doctor, may I introduce you to Colonel Rigby"

The stern, but rather young, man stood next to Kate nodded his head at the Doctor. He didn't salute. Clearly, the Doctor thought, this man would go far. Kate went on to tell the Doctor and Thomas how Rigby was a highly motivated, highly professional individual and could be completely trusted by the Doctor. There was an odd knot forming in the pit of Thomas' stomach. Usually when people were introduced to him as 'someone he could trust', the opposite in fact was almost universally true. Thomas' doubts didn't seem to be unfounded as Rigby was staring at Thomas with the intense gaze that Oakley used to bestow on him. The Doctor appeared to be oblivious to this, ushering the group, now laden with copper wire, into the library and down to the Geography floor. UNIT had already cleared the entire section of the library of students who seemed all too keen to have an excuse not to languish in the building for a moment longer than was absolutely necessary. When the group arrived at the affected bookcases the whispering was more intense than ever.

"We had to wrench a book from one girl's hands when we came here" Kate said grimly "Almost went the way of the porter"

The Doctor turned off the lift so no one could access the floor. The only way up and down now was a small spiral staircase to the next level.

"Kate, Osgood, Rigby" the Doctor addressed his team, clapping his hands together "I need you to attach the ends of these copper spools to these four rows of bookcases. Thankfully they are metal. If they had been wood, well, we don't have to think about that really but lets just say that we would have been in for a very long night, powering ourselves with RedBull and ProPlus tablets surviving only on chocolate fingers. Oh I miss university…"

Rigby and Kate exchanged puzzled looks. The Doctor threw his psychic paper to Osgood who caught it deftly with her free hand.

"Osgood, you've graduated from scientist to carpenter. I want you to create an entirely insulated platform for you all to jump on at the opportune moment" the Doctor saluted at Osgood and she returned it "You will know the opportune moment as you will get a message on the paper. Its on silent at the moment so will only vibrate. Meanwhile, whilst you are busy prepping this department for literally, the biggest shock that it will get in its life, Thomas and I will run the spools up to the roof, creating an unbroken link from the top of the building to the bottom"

"Sorry, you're going to run to the top of a building, holding at least two very very heavy copper wire spools?" Rigby asked incredulously.

"Yes…" the Doctor replied, walking backwards already reeling out one length of copper. Thomas followed suit.

"Well" Rigby said "Are you sure you're up to it?"

What followed was perhaps the most uncomfortable silence in all of human history.

"I'll pretend you didn't say that" the Doctor replied, somewhat tersely, straightening his back as he did so. If looks could kill, the side glance that Kate offered Rigby would have meant his next of kin would be picking out readings for his funeral as we speak. But it was Osgood who knew what Rigby was really trying to avoid the Doctor doing. She knew that it was a risk to send the Doctor alone with Thomas. But Kate obviously trusted the Doctor's judgement far more than she did because she let the pair go.

"This better not go wrong otherwise we will have a nightmare on our hands" the Doctor called back over his shoulder as he and Thomas ran towards the staircase, copper wire trailing behind us.

Kate's face suddenly drained of all its colour. Osgood and Colonel Rigby looked equally panicked. How did he know?

"N-nightmare" Kate managed to get out whilst running through a dozen scenarios of how UNIT could possibly get itself out of the mess that it was about to be hurled headlong into.

"Yes…isn't that something that you can use to call something unpleasant?" the Doctor's voice fading slightly as he ascended the spiralling staircase, Thomas hot on his heels. All three UNIT members looked visibly relieved. He literally meant _a_ nightmare. Not _the_ Nightmare.

"That was close" Osgood said, shaking her hands as if she was ridding herself of pent up stress.

"It was too close" Rigby said, casting Kate a knowing look "He might be on our side if we told him"

"No. He wouldn't. He wouldn't understand. They fought in the Time War. They're unlikely to get on now. But I agree it was too close. We need to re-open talks. Particularly if what we suspect is true. I told Oakley earlier that we need all the help that we can get with this and I wasn't lying. I'll worry about crossing moral lines at a later date when I feel much safer about the future of the planet" Kate said, picking up the ends of copper wire and a soldering iron "Lets just focus on what we have to do now. Make these joins and attach the branches of wire to the bookshelves. The sooner this is dealt with the better I feel"

Rigby nodded in agreement and Osgood took a puff of her inhaler. It had been a hell of a day but the young scientist felt that this was just the beginning of something far greater and far darker. Whilst she could agree with UNIT's actions, it didn't stop her from feeling a little anxious about the precarious alliance that had been made. Just as she was picking up a reel of copper wire, she thought she saw something move at the corner of her eye. Poking her head around an adjacent bookcase, her heart jumped. There was a man, dressed in black, staring at her.

"It can't be…"

But before Osgood could call out to the man, he turned on his heel and darted around the corner. Osgood followed. But when she reached the corridor it was completely clear. He had disappeared.

—

On the roof the Doctor and Thomas were busy attaching the wire to the building's lightning rod. The grey rain was coming down in sheets, making a pleasing sound as it landed on the stone roof of the colossal building.

"They think you have something to do with this, Thomas" the Doctor was speaking so softly and quietly that it made Thomas, for some reason, very sad. Thomas waited for the Doctor to continue talking, press Thomas and force some kind of a confession. But it never came.

"Thanks" Thomas said, smiling slightly.

"For what?" said the Doctor, confused. He couldn't cope with this sudden flip-flopping about in a human's emotional tone.

"For not asking if I did" Thomas replied "Its nice to be trusted"

"Good" said the Doctor, not quite knowing what the appropriate response to that particular statement was. "Can I talk to you about lightning strikes now?"

"Yeah, go on" said Thomas, turning back to face the library's lightning rod.

"The lightning will strike the rod here. Lightning, as any primary schooler will tell you, is electricity. And copper, again you can check with a primary schooler about this one Thomas, is a conductor. By extending the conductive channel down to the affected area of the library we can hijack the current and overlay the code that UNIT sent to us. Therefore, in one fell swoop, we can re-write the code of hundreds and hundreds of books. As the majority of the books will have the new code, the rest will follow. It might take a while for the full effect to trickle through to all the books but the immediate danger will be gone and we can all get on with our lives" the Doctor was busy wiring the sonic screwdriver into the copper laid out on the roof.

"Won't we get zapped?" Thomas asked, cautiously eyeing the copper length now stretched along the roof and disappearing down the access hatch.

"No we'll be fine. I've made sure that the central copper wire going down to the Geography department isn't touching anything that can conduct electricity. We're perfectly perfectly safe. For once. It won't last I'm sure" the Doctor stood back, his work complete "The UNIT lot downstairs are lacing the copper into the book shelves affected"

The Doctor pressed a button on the sonic screwdriver and ushered Thomas towards the lower platform of the roof.

"And now we wait?" Thomas asked, cleaning the grey rain from his glasses on the bottom of his shirt

"And now we wait" the Doctor confirmed, trying to blot out the memory of last time that he had tried to use electricity to bring a threat to the Earth into submission. Gelling his hair like that really had been a mistake.


	10. Chapter 10

**Thanks for reading along/favouriting/following/reviewing! Only two chapters left after this! Have great days, A **

Down on the Geography floor the UNIT team had finished laying the wooden floor panels that would act as an insulator when they stood on them. Just to be on the safe side, Osgood had ordered that rubber should be laid around the edges of the platform. The ends of the lengths of copper that the Doctor and Thomas had run upstairs to the roof were now wound through the offending bookcases. Each UNIT worker acted with extreme caution, careful not to touch any of the books or be too drawn in to listening to what the fervent whispers were saying. The problem was, the more curious you were about the books and their contents, the more appealing they became. The urge to pick them up and read them was almost an overwhelming physical sensation. It was only those UNIT soldiers and agents with the strongest wills that were permitted to plunge to the very depths of the section to lay the wire.

Once all non-essential members of staff were dismissed, only Kate, Osgood, Rigby and a handful of Rigby's men remained. They stood silently on Osgood's platform, waiting for a message from the Doctor. Although they were well into the centre of the building, they could hear the faint sounds of a ferocious storm outside. Kate prayed that the Doctor knew what he was doing.

Suddenly the lights flickered and the psychic paper buzzed.

"Get clear"

—

The storm was reaching its crescendo. Above Thomas and the Doctor the dark clouds had thickened once more, all light from the sun now completely blocked. The only light was coming from the white bolts of lightning, cutting across the sky in their jagged forms. One was yet to hit the tower, but it couldn't be long now. The wind whipped around the two men huddled on the lower platform, desperately trying to protect themselves from the relentless onslaught from the elements.

Eventually a bolt struck the tower, lighting up the Doctor and Thomas. The younger boy's face had a look of pure glee whilst the Doctor looked stoically on. The crackle of electricity coursing through the copper rushed past the Doctor and Thomas and down to the floors below. On the Geography floor the UNIT team could hear the energy approaching them. Within a couple of seconds this would all be over. And maybe, just maybe, they would find out who was behind this unusual, almost incomprehensible attack.

The crackling intensified as the electricity ran through the metal bookcases before being Earthed on the wooden panels below, the Doctor's code being rewritten into the volumes on the shelves. Hundreds and hundreds of books were charged and ready to go with the now innocuous Lire. They wouldn't whisper for many years to come. Or so Kate hoped.

Back on the tower, the Doctor was moving to dislodge the sonic screwdriver from its mounting. Scrambling onto the upper platform, he just managed to reach the device when the sky was illuminated once more. Another bolt of lightning had hit the tower. The Doctor yelped as he yanked the copper wire from the lightning rod and jumped backwards off the platform, landing on his back, sonic screwdriver in hand. Thomas jumped up and ran to the Doctor, almost slipping twice as he did. When he reached the older man, the Doctor was already beginning to prop himself up but Thomas could tell that he had landed hard and somewhat awkwardly.

"Are you alright?" Thomas shouted over the thundering rain landing on the roof

"Yes!" the Doctor replied, pushing himself to a standing position "I managed to disconnect the copper breaking the connection but we need to go downstairs to make sure it hasn't rewritten our good work"

"Your good work don't you mean?"

"I like you Thomas" the Doctor grinned "Keep talking like that and you'll go far"

—

Wave of ink from the books forms a giant hand reaching out - likening to hand reaching out in literature

Black ink seeped out of the books on the shelves and pooled on the floor between the

The room was eerily quiet. Only the crackling of Rigby's waistband radio could be heard. Slowly, the ink began to flow towards UNIT, gathering speed as it came closer to Osgood's wooden platforms. It rose to meet the scattering members of UNIT, forming a hand, reaching out to touch them. The ink structure hovered over Osgood but before it could touch her it collapsed, crashing down into a still perfectly reflective black pool on the floor.

On the spiral staircase, the Doctor lowered the sonic screwdriver.

"Is that it?" Kate shouted to the Time Lord "Is it over?"

"Yes, yes I think so" replied the Doctor, walking over to the slightly shaken UNIT team "The ink is fine. Its completely benign now. The Lire won't visit the human race now until, well, until it is invented. The second wave of lightning might have muted the neutralisation somewhat though. But only to the extent that every now and then you might hear a slight whisper. But nothing dangerous"

"So, if I had an exam tomorrow and put a book under my pillow to try and learn, it might actually work?" Thomas asked hopefully

"Yeah it might. But I wouldn't abandon traditional revision techniques just yet"

"Any idea who is behind this then?" Thomas asked, surveying the pool of ink in front of him

"I'd love to say yes. I'd really really love to. But I can't. I don't know now but I am definitely working on it. I also need to work out why they were here. I mean, it was hardly overtly threatening in the grand scheme of things. Its a pretty unusual way to conquer Earth I mean"

"I guess so" Thomas said, wandering towards the UNIT clear up team who had just entered the room "Better go and give them a hand"

Osgood watched Thomas leave the Doctor before approaching the older man. She had a lot to say to him about herself and her own return, but now was not the time.

"Its almost as if they were put here to lure you in maybe?" Osgood interjected, sidling up to the Doctor who have her a very puzzled look "Sorry, forget I said anything. Doctor, just, please, think carefully about this" Osgood said, in as caring a manner as she could manage without drifting into patronising. "I know that you miss Clara but -"

"I know I made mistakes with Clara. I know I made mistakes with all of them. I certainly made mistakes with you. I didn't always treat them right. I lied to them. But I won't be like that with Thomas. I won't lie to him. The TARDIS made me land here today. It brought me to Oakley's office today. When Thomas was there. Sometimes I don't think that the universe speaks to me. But sometimes I think it does. I just have this feeling that if I go along with this, something good will happen. I can just feel it" the Doctor was buzzing with an excitement that Osgood knew she would have to quell somehow. She cast a glance at Thomas who was now working with UNIT soldiers to cordon off the ink stained library floor. He seemed innocuous enough but there were too many coincidences but there wasn't yet any concrete proof of anything. Just very strong hunches. The closest thing they had was a call from Oakely nearly a year ago now when he started teaching Thomas. There was something about the entire situation that did seem a little off to her. How this boy could be a scheming megalomaniac was quite beyond her. He seemed shy and somewhat awkward. But with a jolt she remembered that the Doctor was also a little awkward and had the same trait of being both proud but also a little embarrassed by his intellect and whilst the Doctor was a great man, capable of saving worlds, he was also capable of carrying out terrible deeds, the consequences of which were still reverberating through time. And Oakley himself could hardly be put above suspicion. He definitely fitted into this picture somewhere although she was struggling to find out exactly where. Absentmindedly she thought this entire business was like one of those pointillist paintings. The closer you were to it, the more it just looking like unconnected dots of random colour. But when you stood back, when you got enough distance, everything became clear. Thats what she needed, some distance, just to figure out exactly what was going on here.

"But" she began tentatively, knowing was about to step on some very risky ground. Just as she was about to expand on her point, Rigby strode up to the pair and whispered something in her ear. The Doctor leaned in slightly, trying to catch what it was, but he didn't hear anything. He straightened back up again and frowned. There was definitely something that UNIT wasn't telling him.

"Rigby?" the Doctor asked "Have you worked out who was behind setting up the Lire?"

"No. Not as yet. But we have a hunch. If you will excuse Osgood and I. It was a pleasure meeting you. I'm sure that we will see each other again in the very near future." One again Rigby nodded to the Doctor before leaving him, Osgood in tow.

But the pair had not got half way to the spiral staircase when the noise stopped them.

There was a low thumping sound, like lots of books landing on top of one another. The Doctor was watching in astonishment as all of the now blank books tumbled off their shelves and flipped open. For a moment there was utter stillness. Not even the UNIT soldiers had reacted and readied their guns, training them on the pile. They were too stunned. The only person in the room who knew exactly what was going to happen next was Thomas.

"Not again" he said under his breath. As soon as the Doctor heard this, his impeccable hearing picking it up even half way across the room. He started to run towards Thomas, reaching into his pocket for the sonic.

One or two pages jumped up very slightly at first and Thomas shouted at UNIT to get back. It seemed an overreaction to the incredibly small amount of movement and not everyone responded But within the minute the room had almost cleared of UNIT members. The small movement grew and grew, the paper gaining more and more kinetic energy and they were defiantly converging on Thomas. Thomas tried to scramble away from the paper but once more he was caught in a whirlwind of papers, flicking around him and blocking anyone out.

Outside of the revolving ball of paper the Doctor was struggling to find the correct setting on the sonic screwdriver. Whatever he used, it just didn't seem to work. With a growing sense of distress, the Doctor saw that some of the white pages were now tinged with red. The whipping sound of the paper only seemed to be getting stronger. Thomas was flighting in the paper, trying to battle against the wall of white that just seemed to be getting denser and denser. He now could only vaguely see the steel bookcases and mahogany walls of the library through the blinding white of the paper. Is this how he would die? Encased in the purest innocent white? Killed by his own pursuit of knowledge? In some ways, it seemed quite poetic.

The Doctor was now frantically going through settings. Time was running out. He shouted in frustration. Why was nothing working?

"I thought you said that the Lire was no longer a threat" yelled Kate over the roar of the paper

"I did" the Doctor shouted back, trying yet another incorrect setting "This isn't the Lire. This is something else entirely!"

"Well what is it?"

"I don't know! Its not my prime concern at the moment. I just want to stop it!"

"Won't knowing what it is help you stop it?"

"Oh shut up!" the Doctor bellowed, whacking the screwdriver against his leg. There was a louder buzz from the sonic screwdriver and the Doctor thrusted the device at the whirl of paper. "Ah! Yes!"

Painfully slowly the rotating paper began to slow and fall about Thomas. But as the student moved towards the Doctor a wave of energy coursed through the paper and exploded outwards, knocking the Doctor and most of the UNIT operatives to the ground, scattering the papers across the room.

As the final maelstrom of pages died down the Doctor found that he now had far more questions than answers. Still sat on the floor he did a quick sonic scan of the now lifeless pile of paper. Nothing. Thats all that it was now. A pile of paper. He looked at Thomas sat next to him, gasping for breath and wiping the sheen of sweat off his forehead. The paper had definitely come for him. As it had earlier that day outside Thomas' room. What was so special about Thomas? And what was making the paper move?

The Doctor threw himself backwards into a lying position on the library floor, sending up a plume of papers around him. The library was silent once more save for the rustling of the UNIT agents moving in to start a colossal clear up. Next to the thousand year old man, Thomas was sat running his hands through the now benign papers, laughing silently to himself.


	11. Chapter 11

**Just a short chapter...not long left now! **

The Doctor and Thomas stood outside outside the TARDIS. Although the storm had passed the sky remained cloudy and the air thick and smelling slightly of rain. A light wind passed through the oak tree behind the TARDIS, the leaves rustling gently. A calm end to an extraordinary day.

Thomas was stood with his hands in his pockets, head bowed slightly. Since coming down from the roof he had been worrying about what happens next. Does the Doctor stay? Does he stay with UNIT? Does he get in his blue box and go somewhere else? Can he go with him? Now, stood opposite this extraordinary man, for once in his life Thomas did not want to be left alone.

"Well, all done here. Off to somewhere more interesting with people who are fare less stupid. Pudding brains the lot of you" said the Doctor, stroking the TARDIS door as he spoke. Thomas didn't know how to reply. So this was it then. The final farewell. Thomas nodded slightly and took his hands out of his pockets and offered one to the Doctor. The Doctor looked at Thomas' hand and took a step back.

"You were meant to shake it" Thomas said in a hushed voice as he lowered his hand and put it back in his pocket "Like much of the world, in Britain a firm handshake, lasting a few seconds, is the common form of saying goodbye, for all business situations and most social situations too. Well, according to Debretts anyway"

"You have a very good memory Thomas" the Doctor said in a level tone

"Yeah" Thomas' voice seemed to get even quieter. His cleverness, his love of learning had landed him in a lot of trouble in the past. It had distinguished him from his peers leaving him at the top of the class but also friendless. People were scared of him, or at least his intellect.

"You're not proud of it though, why?" the Doctor asked, head cocked slightly to the left

"Well, I guess its…wait, how did you know I'm not proud of it?" Thomas replied. No one before had ever taken an interest in Thomas' feelings about his intelligence. People always assumed that everything in life came easily to him. No-one assumed that he had to work at anything. Teachers and parents and peers always expected that he would excel. If he ever said that he was struggling, no one believed him. "Oh you'll be fine" they said "You're clever, you don't even have to try". This only added to Thomas' sense of isolation that was rapidly becoming more and more of a real thing. At home Thomas had no-one. At Cambridge he had Harley but only just. She had lots of friends and Thomas knew that however nice she was to him, she didn't regard him as a best friend. The feeling of being lonely in a room with a friend was worse than feeling lonely in a room on your own.

"Because when I was younger, I wasn't proud of my intelligence either. I hid it thinking that I could be someone that I wasn't. I wanted to be strong and quick and brave. It turns out that bravest thing I ever did wasn't fighting, or winning races. The bravest thing I ever did was be myself. As awfully corny as that sounds. But truly, the bravest thing I've ever done was running away. And I'm still running now" the Doctor took a step forward and offered his right hand to Thomas "According to Debretts, handshakes are also a common form of face-to-face greeting"

Thomas took the Doctors hand and shook it. Unlike Harley's hand, the Doctor's fitted well in his.

"Come with me" the Doctor said. It wasn't so much of a request as a demand. Thomas nodded and smiled. This was it. The beginning of something extraordinary. Something that people only dreamed of. Once again, the Doctor held open the TARDIS doors for Thomas to enter. The younger man entered the TARIDS, still with a look of wonder on his face. He couldn't believe his luck. It felt like all his life had been working towards this moment.

"Now, wheres the first place you want to go?" the Doctor's arms were outstretched as the TARDIS closed her own doors behind him.

Thomas looked around at the Doctor, jaw slack. The first place? That means that he would be going to more than one place. It looked like he was in this for the long run. Thomas really hoped that there wasn't a probationary period that he would somehow fail. After a moments thought he knew exactly where he wanted to go. But there was something that he wanted to see first.

The Doctor placed his hand on a bank of levers and pulled down hard. The TARDIS lurched as the engines wailed into life. The TARDIS was louder this time, calling out to someone it seemed, as the familiar sound of the engines drowned out the Doctor's shouting to Thomas. The TARDIS dematerialised, unnoticed by the pack of students cycling past on the way to lectures, supervisions and study breaks in Starbucks. Their young lives full of potential, all on the verge of something brilliant. Or at least they hoped they were. But there were two people who sat up a little straighter as the TARDIS' engines engaged. In his office Oakley rushed to the window to see a deserted Great Court in front of him. He didn't know what he was expecting to see and he felt a little foolish for jumping up as he had. Oakley looked back to the open file on his desk, newly delivered to him from UNIT. He felt angry that they had concealed from him their plans and had hidden away the most precious thing in the world to him.

Across town, Harley Lauda was sat with her latest model on the table in front of her when a wave of nausea came over her. Getting up from her work bench, she grabbed her sunglasses resting on the table and left the studio. Climbing the spiral wooden stairs to the roof Harley slid the sunglasses onto her scarred face. Walking through the door onto the decking the roar of the TARDIS' engines seemed to surround her. Harley's hand hovered over jeans' pocket. But before she could think any further about what all this meant, Harley felt a hand on her shoulder.

"Harley" the voice said "You just took off there. Are you alright?"

Harley turned around to see one of the studio's supervisors. It was the American woman. Mia, Harley remembered that she was called.

"I'm always alright" Harley replied, smiling slightly and taking a seat on one of the benches running around the deck. Mia sighed as she watched Harley. Of all of Mia's class, it was Harley that interested, and worried, her most. Harley was talented. No-one could deny that. Her forte was designing large classical buildings. Harley had once confided in Mia that she wanted to work in restoration rather than create new buildings. Mia said that this was something that Harley should pursue and had gone on to arrange a months work at Liverpool Cathedral shadowing the team of architects working there, maintaining and preserving the fabric of the building. Harley had even brought back a piece of sandstone that she had been allowed to practice carving on by the stonemasons. For a first attempt it was remarkable. It was evident that Harley was very proud and her enjoyment in her own work and the fact that Mia was obviously proud of it too was almost childlike. For a brief moment Mia caught a glimpse of a much younger Harley and it broke her heart. Whatever had happened to Harley was obviously horrific and made her stop showing any form of vulnerability. Mia got the feeling that Harley had had to grow up very quickly. Even when Harley was struggling, she said she was alright. When Harley was knocked off her bike just outside the department bouncing off the hood of a car and landing on her already crippled left arm, she got back up, dusted her self off and said she was alright. Anyone could tell from a mile off that she wasn't. But she refused to appear to need help. Mia supposed that it was because somewhere in Harley's mind asking for help equated to weakness and weakness was a failure. Possibly because it could be exploited.

Mia moved to sit next to Harley on the bench.

"I'm alright Mia" Harley said not looking up "You don't have to sit with me"

"Harley" Mia said, reaching out to put her hand back on Harley's shoulder "you can't go through life without somebody to sit with. Its too hard. Everybody deserves someone who wants to sit with them"

Thousands of miles above the Architecture Department, Thomas was stood leaning on the doorframe of the TARDIS, its blue doors thrown open to the deep black sky. The Earth looked like a blue marble against a backdrop of stars. Thomas stretched out his hand and covered the Earth with his thumb and held it there. How small it really was. In the grand scheme of things, it really was small, crushed by the thumb of Thomas. But on that tiny little orb were millions of lives. People born and dying. People doing big things like climbing mountains and little things like the washing up. There were people generating theories about this little Earth, discovering new things everyday and pushing towards breakthroughs in science, engineering and medicine. But equally there were people on the eighth hour of their Netflix marathon.

"Travelling with you, is it always going to be dangerous" Thomas asked, back to the Doctor still facing the Earth below

"Mostly" the Doctor replied

"Is it always going to be this fun?" Thomas was smirking slightly this time

"Always" the Doctor's voice clear, confident. Everything that Thomas wanted to be.

Thomas turned his back to the Doctor and looked out to the Earth again. He needed to get a grip. Why now was he so uncertain? But he guessed it was quite a normal reaction when one was leaving one's home and embarking on a journey that would push him to his limits. But he would learn so much. He would travel to so many places. And he would get to spend time with the Doctor.

"So, Thomas. What do you say, are you in or out?" asked the Doctor "Remember, people get killed in the middle of the road"

"I'm in" Thomas took a step back and closed the TARDIS doors behind him and turned around to face the Doctor. Things would never be the same again.


	12. Chapter 12

**So this is it! The last instalment in Thomas and the Doctor's first adventure. Thanks for reading along as well as reviewing, favouriting and following. I'm glad you like Thomas. The link to his next outing with the Doctor is at the bottom of this chapter. Whovian love from Deutschland, A **

Kate was back at the Tower of London, still running a fine tooth comb through the data that the team had collected in Cambridge two weeks earlier. Back in the vaulted chambers of the Tower, Kate thought that she could think more clearly. So far, all of the evidence was pointing to the conclusion that Kate didn't want UNIT to make. The implications didn't bear thinking about.

Kate leant back in her chair and ran a hand through her hair, wondering what her next move should be. There was a slight rap of knuckles on the glass door to her office and Kate could see that Osgood was waiting outside, a concerned look on her face and a manila folder in hand. Kate motioned for her to come in.

"Have you got a moment?" Osgood asked, clearing her throat slightly before she spoke. No matter how long she had worked with Kate, she still got a little nervous when she was about to break bad news. Particularly news like this. Osgood drew up a chair and sat opposite Kate, opening the folder and spreading its contents out on the desk in front of her. Just the mere opening of these documents seemed to lower the temperature of the room and bring a rather uncomfortable atmosphere. Kate glanced down at the papers in front of her and felt a knot in her stomach.

"M'am, before we begin, perhaps Colonel Rigby should be here?" Osgood suggested. Kate nodded tersely and made a quick call, asking for the Colonel to be brought up to her office. Whilst Colonel Rigby was young, he had a clear head on his shoulders and could be trusted to carry out even the most sensitive and controversial missions with discretion and efficiency. There may well be people older, more experienced and higher up the ranks than him, but for this job, Rigby was suitable. He came into Kate's office, saluted and took off his hat before sitting down. His back was ram-rod straight which made Osgood try to straighten up slightly. The trio sat in silence for a moment. No-one wanted to be the first person to speak. Eventually Osgood plucked up enough courage to start, spreading the documents in her folder out onto Kate's desk.

"Its what we thought it would be. But not who" Osgood said. Kate and Rigby looked puzzled. Osgood took a deep breath and continued "Time Lord, yes. But, like I said, not the one we expected"

The was another silence as Kate pinched the bridge of her nose, scanning the information in front of her.

"Are you sure?" Colonel Rigby asked, shifting a little in his seat

"Yes. It explains everything. The time travel, the knowledge of the Lire, the disappearances. We have evidence too." Osgood rifled through the documents on the desk and showed Kate an x-ray photo of Kate's discussion with the Doctor, Oakley, Thomas and Harley under the arch taken from a camera that UNIT had placed on the roof. Osgood pointed to the _two_ figures with _two_ hearts. Only one of them was the Doctor.

"So its not the Master, or Missy?" Kate asked

"No" replied Osgood "We managed to get a DNA sample, or well, the Time Lord equivalent. The marker for the Master doesn't appear"

"So, its an unknown Time Lord we are dealing with?" asked Rigby, who was now inspecting the x-ray.

"Not entirely unknown" Osgood looked to Kate "They've tried to hide who they are. They've done it very well I might add. Its actually very impressive. We're not one hundred percent certain, but we think that the Time Lord in question is this person"

Osgood proceeded to hand Colonel Rigby and Kate two identical pieces of paper. The pair took a minute to read through the information.

"Do we refer to them as Time Lord or Time Lady?" Rigby asked, placing the profile back on the desk and resting his hands in his lap.

"I hardly think that semantics are our biggest problem at this point, Rigby" Kate said, casting the Colonel a cool look "You said disappearances? I wasn't aware that there were any"

"It came up in one of the interviews with the porters. They said that a student, Ezekiel Davies, had been missing for a few weeks now. He had been Thomas O'Mara's lab partner. That was the only reason that we found that out during questioning. We hadn't specifically asked about missing people. We are assuming that more have gone missing so we are widening the search" When Osgood had finished speaking Kate stood up and walked to the the glass wall of her office that was suspended at the top of the stone chamber. Looking down to the floor below, she could see UNIT's brightest and best working on any number of dangerous and highly secretive projects. Everyday they worked to keep the general public safe from enemy threats. Hidden heroes. The lot of them.

"Does the Doctor know?" Kate asked Osgood, her back still facing the scientist and the Colonel

"If he does he isn't letting on" Rigby cut in, picking off a minute piece of fluff from his uniform.

"How could he know?" Osgood replied, getting up and walking over to stand next to Kate "I mean, its not like they look like they used to. The Doctor didn't even recognise Oakley so how he was meant to recognise her…"

"Right, we need all the help we can get for this one. I know I keep saying that but its true. Get everyone on this. And I mean everyone. Anyone who has ever breathed near this kid, I want them here. We need information. All that we can get. And we need to find out how we missed this. Because this is colossal" Kate gathered the papers on his desk back up and placed them in the folder, handing it back to Osgood.

"M'am, do you want to speak to —" Rigby started but was cut off by Kate's abrupt response. She knew exactly who he was talking about.

"Bring them in by force if you have to Rigby. No excuses." Kate motioned for Osgood to lead the way and Kate followed, Rigby not too far behind, hands in pockets and a determined look on her face.

—

The service was drawing to a close. Saturday night vigil had become a ritual for Harley and tonight was no different. It wasn't that she particularly believed in anything that was being said, it was just that it gave her a moment of calm that was hard to find in a life as busy and stressful as hers. But despite this, she wouldn't trade her life for anyone else's. Her difficulties and pain were as much a defining feature of her character's development as her victories and laughter.

The Chaplain had begun a small speech about the nearing of the end of term and the coming of Easter. Harley wasn't really listening. Her mind was elsewhere with the growing list of things that she needed to do. As the opening chords of the final hymn started, Harley looked up to the organist sat on a raised loft above the congregation at the back of the chapel, his bright red cassock a stark contrast to the black pipes of the organ. As she lowered her gaze, she saw a man in black stood outside the chapel doors. He was armed. Harley snapped her head back to face the congregation on the other side of the chapel. She had declined Kate's request to come to the Tower, outlining exactly her reasons why. And this was the response?

The choir began to sing. And Harley began to think.

_When I survey the wondrous cross_

_On which the Prince of glory died,_

_My richest gain I count but loss,_

_And pour contempt on all my pride._

Outside the chapel, Colonel Rigby was stood with seven other men. They were dressed all in black, masked and armoured for full combat. There were a further twenty men spread around the chapel. He made the decision that Harley should be able to see him through the doors. He wanted her to know that they were there and waiting for her. He wanted this to go as smoothly as possible and as quickly as possible. Maybe if she saw that they were armed, she would give herself up and come quietly. After all, they knew that she wasn't carrying a weapon. They had observed her going into the chapel half an hour earlier in a pair of shorts and a jumper, neither of which had pockets big enough to conceal anything that would be of any use. Harley Lauda was cornered.

_Forbid it, Lord, that I should boast,_

_Save in the death of Christ my God!_

_All the vain things that charm me most,_

_I sacrifice them to His blood._

Harley reached into her short's pocket and pulled out the small silver fob watch and chain that she had taken to carrying about with her and turned it over in her hand. She stole it many years ago. So long ago that she couldn't remember how old she was. Harley clipped the end of the chain to the waistband of her shorts. She didn't want it to get lost. Harley apologised to the person sitting next to her for inadvertently elbowing him whilst she did this. Harley glanced back towards Rigby and sighed. Did they really want to do this? Harley leaned back in her seat and saw two other figures in black and both armed. Apparently they did.

_See from His head, His hands, His feet,_

_Sorrow and love flow mingled down!_

_Did e'er such love and sorrow meet,_

_Or thorns compose so rich a crown?_

Harley exited her pew and bowed towards the altar, turned on her heel and walked calmly towards the chapel doors. Rigby could see her walking towards them and he could hardly believe his luck. Was it really going to be this easy? This was, allegedly, one of the greatest tacticians of all time. Surely she wasn't giving herself over? After all, she had not replied to Kate's earlier offer of coming to the Tower without the use of force. Rigby had prepared his men for a fight and now he was almost disappointed that there wasn't going to be one.

As she drew closer, Rigby was taken aback by just how young she looked. He'd read the brief report on her. UNIT didn't have much information but what they did have was devastating. All that was available were second hand accounts of her work. There were no eyewitnesses. No survivors. At least, none that had made it to Earth anyway. Well, apart from the Doctor's account of course and that was damming enough.

Rigby adjusted the grip on his gun slightly as Harley's face became clearer. She smiled slightly at him. It wasn't callous. Or sly. It was almost sad. Rigby couldn't square this person with the person who had killed all those people. It just didn't fit. Something wasn't right about the whole picture.

But before Rigby could think any further on this, the wooden chapel doors began to close. Rigby dashed forward, just making it through the gap with three of the men who were in the corridor with him. But in the confusion, he had lost sight of Harley. He was now stood in the back of the chapel, looking about wildly left and right, for her. But she wasn't anywhere. She had definitely gone. And how on earth had she made those doors close? Just as he was about to go back to his men outside, a voice cut through on his ear piece:

"Female figure exiting the chapel through side door. Now in pursuit"

Rigby looked towards the altar and said a small prayer of thanks to whoever was listening upstairs. If he'd have looked skywards to say his prayer, he may have spotted the mistake that he was about to make.

"Mobilise all units" Rigby said, signalling for his men to follow him back out the door and into the gardens behind the chapel.

_His dying crimson, like a robe,_

_Spreads o'er His body on the tree;_

_Then I am dead to all the globe,_

_And all the globe is dead to me._

From the organist's balcony, Harley looked down to see the men leaving the chapel as swiftly as they had come. They had spotted somebody. Harley couldn't believe her luck. She rapped the wood of the balcony with her knuckles and walked towards the stairs, waving to the slightly started organist as she went. How very British it was that he still kept playing even when an interloper had managed to climb up to his loft.

Harley took the stairs two at a time, bounding down them towards the court and the cool night air. As she left the chapel, she looked back to she that she wasn't being followed and smiled when she saw that the path ahead of her was clear. Harley knew UNIT's tactics; she still had time to finish her work in the college library. Not much time, but enough for what was needed. It was evident that this would be her last night in Cambridge for a long time.

As she walked towards the white stone building, the final chorus of the hymn in chapel could still be heard. Grinning as she went and punching the air above her head, Harley joined in, belting out the final verse. For now she could enjoy herself. For now she could relax. It was a small victory, but one that Harley was glad to win. Later tonight she would open the watch. Once more, as the silver top would flip open, her tall twisted figure would be enveloped in white tendrils of light and she would resume her true position in the universe. Her convictions unshaken. Her sense of duty strong. And her loyalty to her role driving her forwards with a stoicism and bravery unrivalled. Except perhaps by one man. The man who gave her her scars. It was time to read up on John Frobisher. Bridget Spear's statement looked like it was going to be an informative read. It was time to catch up with the Doctor and the TARDIS he claimed as his own.

_Were the whole realm of nature mine,_

_That were a present far too small;_

_Love so amazing, so divine,_

_Demands my soul, my life, my all._

**Thanks once more, particularly to bored411 who has followed Thomas from the beginning. Here's his next adventure s/11424778/1/The-Library-of-Alexandria **


End file.
